RMA_0113	RMA_0138	Y	Y	Y	RMA_0095	RMA_0140
	RMA_0113	2	13	-1.117969	OmpW family outer-membrane protein
	RMA_0114	2	11	-1.061684	S-adenosylmethionine transporter
	RMA_0115	3	10	-1.064957	proline/betaine transporter
	RMA_0116	3	11	-0.798346	hypothetical protein
	RMA_0117	1	9	-0.522156	*preprotein translocase subunit SecG
	RMA_0119	0	10	-0.565699	cell surface antigen Sca2
	RMA_0120	-1	8	0.915917	cysteinyl-tRNA synthetase
	RMA_0121	0	9	0.737881	30S ribosomal protein S2
	RMA_0122	2	10	0.646582	elongation factor Ts
	RMA_0125	1	10	-1.812576	3-deoxy-D-manno-octulosonic-acid transferase
	RMA_0126	3	11	-2.418590	hypothetical protein
	RMA_0127	2	10	-2.203619	aspartate aminotransferase
	RMA_0128	4	12	-3.134821	hypothetical protein
	RMA_0129	2	12	-1.974199	antitoxin of toxin-antitoxin
	RMA_0130	3	12	-0.959645	hypothetical protein
	RMA_0131	2	14	0.578872	VacJ lipoprotein precursor
	RMA_0132	2	14	0.101693	ABC transporter
	RMA_0133	1	15	0.398463	ribose-phosphate pyrophosphokinase
	RMA_0134	1	13	0.431574	alanine racemase
	RMA_0135	0	12	0.252964	ABC transporter permease
	RMA_0136	-1	15	-1.122749	ribonucleotide ABC transporter ATP-binding
	RMA_0137	2	14	-1.342406	hypothetical protein
	RMA_0138	2	14	-1.875816	hypothetical protein
	71#RMA_0115	TCRTETA#Tetracycline resistance protein signature.	34	0.001
		>TCRTETA#Tetracycline resistance protein signature.
		          Length = 399
		
		 Score = 33.6 bits (77), Expect = 0.001
		 Identities = 69/332 (20%), Positives = 120/332 (36%), Gaps = 49/332 (14%)
		
		Query: 68  FFGVIGDRFGRKVALTSALFCMSVPTVLIGILPTYHTIGITATILMICVRILQGLS-MGG 126
		             G + DRFGR+  L  +L   +V   ++   P          +L I  RI+ G++   G
		Sbjct: 62  VLGALSDRFGRRPVLLVSLAGAAVDYAIMATAPFL-------WVLYIG-RIVAGITGATG 113
		
		Query: 127 ALTGSISFVI--EHTSHKHQGFTGSISMSSICSGLLLGSFVSYIVKNILTASQFDSFGWR 184
		           A+ G+    I       +H GF  +     + +G +LG  +               F   
		Sbjct: 114 AVAGAYIADITDGDERARHFGFMSACFGFGMVAGPVLGGLMG-------------GFSPH 160
		
		Query: 185 IPFLLGFFILFAAFYIKKNTHETPNFKNLREQKKILQSPLKKVITNYW--FDILISIFIN 242
		            PF     +    F              L E  K  + PL++   N    F     + + 
		Sbjct: 161 APFFAAAALNGLNFLT--------GCFLLPESHKGERRPLRREALNPLASFRWARGMTVV 212
		
		Query: 243 APGSIIFYLTTIYLVSFLKISRNFTENEVNSLASVSYVIMIAV-----TLLSGYLSDIIG 297
		           A    +F++  +       +   F E+  +   + +  I +A      +L    ++  + 
		Sbjct: 213 AALMAVFFIMQLVGQVPAALWVIFGEDRFH-WDATTIGISLAAFGILHSLAQAMITGPVA 271
		
		Query: 298 RR--KIFVINLIIIIVTTSFLLNNFENGAFTSVIISQLILAILAASYIGPEPALQAEL-- 353
		            R  +   + L +I   T ++L  F     T   ++  I+ +LA+  IG  PALQA L  
		Sbjct: 272 ARLGERRALMLGMIADGTGYILLAF----ATRGWMAFPIMVLLASGGIG-MPALQAMLSR 326
		
		Query: 354 YPTNIRNTALSISYNTATSIFGGTTPLVFEYL 385
		                R   L  S    TS+     PL+F  +
		Sbjct: 327 QVDEERQGQLQGSLAALTSLTSIVGPLLFTAI 358
		
		
	73#RMA_0117	SECGEXPORT#Protein-export SecG membrane protein signature.	56	6e-14
		>SECGEXPORT#Protein-export SecG membrane protein signature.
		          Length = 110
		
		 Score = 56.1 bits (135), Expect = 6e-14
		 Identities = 32/100 (32%), Positives = 55/100 (55%), Gaps = 1/100 (1%)
		
		Query: 1   MIDILLFVHITIAILLIIVILMQR-SGSDGISSISGGNNMGVVSAKTVGNFLTKSTIILT 59
		           M + LL V + +AI L+ +I++Q+  G+D  +S   G +  +  +   GNF+T+ T +L 
		Sbjct: 1   MYEALLVVFLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLA 60
		
		Query: 60  TLFLINAIVLANLSSKKKSDLVSKINEIEENQAENSLPIA 99
		           TLF I ++VL N++S K +      N     + E + P A
		Sbjct: 61  TLFFIISLVLGNINSNKTNKGSEWENLSAPAKTEQTQPAA 100
		
		
	83#RMA_0130	PF08280#M protein trans-acting positive regulator	29	0.037
		>PF08280#M protein trans-acting positive regulator
		          Length = 530
		
		 Score = 28.7 bits (64), Expect = 0.037
		 Identities = 18/52 (34%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
		
		Query: 218 PNTKIYDQIYNIAIDEFLKQNSNKFDIIFSFCGLSFTNNLIEYFNLIYSSLN 269
		           P T+I+ Q+  + + + LK++S   DII ++C L+F+   ++Y  LIY + N
		Sbjct: 250 PQTRIFQQLKKLFVYDSLKKSSR--DIIETYCQLNFSAGDLDYLYLIYITAN 299
		
		
	84#RMA_0131	VACJLIPOPROT#VacJ lipoprotein signature.	235	7e-80
		>VACJLIPOPROT#VacJ lipoprotein signature.
		          Length = 251
		
		 Score =  235 bits (600), Expect = 7e-80
		 Identities = 70/201 (34%), Positives = 104/201 (51%), Gaps = 7/201 (3%)
		
		Query: 57  YDPYEKFNRKVFVFN-SVLDYIILRPLAIGYKNITNDYVKARVNSFVSNVDTLLTAVNYG 115
		            DP E FNR ++ FN +VLD  I+RP+A+ +++      +  +++F  N++     VNY 
		Sbjct: 29  SDPLEGFNRTMYNFNFNVLDPYIVRPVAVAWRDYVPQPARNGLSNFTGNLEEPAVMVNYF 88
		
		Query: 116 LQLNYDKTMKSVWRFLINTTLGIGGLFDVAGKVGLPSNR---QTFGSTLAHYGVAPGPYL 172
		           LQ +  + M    RF +NT LG+GG  DVAG       R     FGSTL HYGV  GPY+
		Sbjct: 89  LQGDPYQGMVHFTRFFLNTILGMGGFIDVAGMANPKLQRTEPHRFGSTLGHYGVGYGPYV 148
		
		Query: 173 VLPIIGSTNARDMTDLVITNYALNPLMYYTHNDFDLGVLAVSTINDRYVVLPFSDYVMKN 232
		            LP  GS   RD  D      AL P++ +      +G   +  I  R  +L  SD +++ 
		Sbjct: 149 QLPFYGSFTLRD--DGGDMADALYPVLSWLTWPMSVGKWTLEGIETRAQLLD-SDGLLRQ 205
		
		Query: 233 STDPYVAIRSALHRAREASVQ 253
		           S+DPY+ +R A  +  +    
		Sbjct: 206 SSDPYIMVREAYFQRHDFIAN 226
		
		
	87#RMA_0134	ALARACEMASE#Alanine racemase signature.	255	1e-84
		>ALARACEMASE#Alanine racemase signature.
		          Length = 356
		
		 Score =  255 bits (652), Expect = 1e-84
		 Identities = 101/361 (27%), Positives = 166/361 (45%), Gaps = 21/361 (5%)
		
		Query: 27  TVEINLSTIKNNYLLLQDICKTSLVGAAVKANGYGLGAVQISKALIEENCRHFFVASSEE 86
		              ++L  +K N  +++     + V + VKAN YG G  +I  A+   +   F + + EE
		Sbjct: 6   QASLDLQALKQNLSIVRQAATHARVWSVVKANAYGHGIERIWSAIGATDG--FALLNLEE 63
		
		Query: 87  GVNLRNALGLDVNILVLNGVFEHDALELI-EYNLTPVLNNLKQIEIWQKFSNLKNRLLPC 145
		            + LR   G    IL+L G F    LE+  ++ LT  +++  Q++  Q  + LK  L   
		Sbjct: 64  AITLRER-GWKGPILMLEGFFHAQDLEIYDQHRLTTCVHSNWQLKALQN-ARLKAPL-DI 120
		
		Query: 146 YLHFNTGINRLGLSSDEIEQLINDRDLLKGLDLQYIISHLAISEEIDNPYNLEQLNRFKA 205
		           YL  N+G+NRLG   D +  +      +  +    ++SH A +E  D       + R + 
		Sbjct: 121 YLKVNSGMNRLGFQPDRVLTVWQQLRAMANVGEMTLMSHFAEAEHPDGISG--AMARIEQ 178
		
		Query: 206 YLQYFPNVKASLANSGGIFLGQDYHFDLARSGAALYGLNPLTKN---------PV-TLKA 255
		             +     + SL+NS       + HFD  R G  LYG +P  +          PV TL +
		Sbjct: 179 AAEGLEC-RRSLSNSAATLWHPEAHFDWVRPGIILYGASPSGQWRDIANTGLRPVMTLSS 237
		
		Query: 256 PIIHLQNLTLDSHIGYNMTFTTKRDSVIATLPLGYADGFSRNFSNQGEVFINSRGVPIVG 315
		            II +Q L     +GY   +T + +  I  +  GYADG+ R+      V ++      VG
		Sbjct: 238 EIIGVQTLKAGERVGYGGRYTARDEQRIGIVAAGYADGYPRHAPTGTPVLVDGVRTMTVG 297
		
		Query: 316 RVSMDLINIDVTDLPPSEIFLGQEAEIIGNYCTPDKIASIIGTIGYEVLTNLGSRYKRKY 375
		            VSMD++ +D+T  P  +  +G   E+ G     D +A+  GT+GYE++  L  R     
		Sbjct: 298 TVSMDMLAVDLTPCP--QAGIGTPVELWGKEIKIDDVAAAAGTVGYELMCALALRVPVVT 355
		
		Query: 376 I 376
		           +
		Sbjct: 356 V 356
		
		
RMA_0237	RMA_0274	Y	Y	N	RMA_0212	RMA_0273
	RMA_0237	-1	11	3.033522	putative 6-pyruvoyl tetrahydropterin synthase
	RMA_0238	0	11	3.492373	dihydrolipoamide succinyltransferase
	RMA_0239	-1	9	2.666523	2-oxoglutarate dehydrogenase E1 component
	RMA_0242	0	9	1.771418	DNA repair protein RecN
	RMA_0243	-1	10	1.892467	DNA uptake lipoprotein
	RMA_0245	0	11	0.725013	chaperone protein DnaJ
	RMA_0246	0	9	-0.680984	molecular chaperone DnaK
	RMA_0247	-2	10	-2.636838	heat shock protease
	RMA_0250	0	14	-3.411055	hypothetical protein
	RMA_0251	-1	14	-3.574304	hypothetical protein
	RMA_0252	0	10	-2.445895	DNA polymerase III subunit delta
	RMA_0253	1	10	-0.449527	ubiquinone biosynthesis protein coq7
	RMA_0254	1	9	-0.252795	cytochrome c oxidase subunit III
	RMA_0255	-1	10	-0.898691	VirB2-like protein
	RMA_0256	-1	9	-2.019881	hypothetical protein
	RMA_0257	-2	10	-1.395101	2,3,4,5-tetrahydropyridine-2,6-carboxylate
	RMA_0260	-1	10	-1.813260	bifunctional penicillin-binding protein 1C
	RMA_0266	1	12	-3.417386	universal stress protein UspA
	RMA_0267	1	11	-2.769960	TRAP-type transport system, periplasmic protein
	RMA_0268	0	11	-0.347818	hypothetical protein
	RMA_0269	0	12	1.276677	ferredoxin
	RMA_0270	0	14	1.717032	chaperone protein HscA
	RMA_0271	0	17	3.937359	co-chaperone HscB
	RMA_0272	0	18	4.282590	ribonuclease HII
	RMA_0273	1	18	4.297488	excinuclease ABC subunit B
	RMA_0274	1	17	3.731539	GrxC family glutaredoxin
	177#RMA_0245	PF06438#Heme acquisition protein HasAp	31	0.006
		>PF06438#Heme acquisition protein HasAp
		          Length = 205
		
		 Score = 31.1 bits (70), Expect = 0.006
		 Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
		
		Query: 71  DAFQNQQSRGGGGNHGGFHPDINDIFGDFFSDFMGGSRRSSRPTSAKVRGSDLKYNLTIN 130
		           D          G N GGF+P      G  ++       +S+   +A + G DL Y L  N
		Sbjct: 29  DVNHRPGQVVDGSNTGGFNP--GPFDGSQYA------LKSTASDAAFIAGGDLHYTLFSN 80
		
		Query: 131 LEEAFHGIEKNISF 144
		                 G   +I+ 
		Sbjct: 81  PSHTLWGKLDSIAL 94
		
		
	178#RMA_0246	SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein s...	150	2e-42
		>SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein
		           signature.
		          Length = 347
		
		 Score =  150 bits (381), Expect = 2e-42
		 Identities = 86/389 (22%), Positives = 148/389 (38%), Gaps = 72/389 (18%)
		
		Query: 34  KKTRNLMGKVIGIDLGTTNSCVAVMEG----KEPKVIE-NAEGERTTPSIIAFANGEKLV 88
		           KK R +    + IDLGT N+ + V        EP V+    +   +  S+ A       V
		Sbjct: 3   KKFRGMFSNDLSIDLGTANTLIYVKGQGIVLNEPSVVAIRQDRAGSPKSVAA-------V 55
		
		Query: 89  GQSAKRQAVTNPRNTIYAVKRLIGRNFIDPMVRKDQGIVPYNIVKADNGDAWVEADNNKY 148
		           G  AK+     P N I A++         PM  KD  I  +                  +
		Sbjct: 56  GHDAKQMLGRTPGN-IAAIR---------PM--KDGVIADF------------------F 85
		
		Query: 149 SPSQISAFILQKMKETAENYLGDKVTQAVITVPAYFNDAQRQATKDAGKIAGLEVLRIIN 208
		              ++    ++++   +         + ++ VP      +R+A +++ + AG   + +I 
		Sbjct: 86  VTEKMLQHFIKQVHSNS---FMRPSPRVLVCVPVGATQVERRAIRESAQGAGAREVFLIE 142
		
		Query: 209 EPTAAALAYGFEKSASKTIAVYDLGGGTFDVSILEIADGVFEVKSTNGDTFLGGEDFDTR 268
		           EP AAA+  G   S +    V D+GGGT +V+++ +   V      +    +GG+ FD  
		Sbjct: 143 EPMAAAIGAGLPVSEATGSMVVDIGGGTTEVAVISLNGVV-----YSSSVRIGGDRFDEA 197
		
		Query: 269 ILNHLIDVFKKENGIDLSKDPLALQRLKEAAEKAKKELSSAVTTD----INLPYITADSS 324
		           I+N++   +    G             +  AE+ K E+ SA   D    I +        
		Sbjct: 198 IINYVRRNYGSLIG-------------EATAERIKHEIGSAYPGDEVREIEVRGRNLAEG 244
		
		Query: 325 GPKHLNIKFTRAELEKLVDDLIEKTIEPCRKALQD-AGFKASDIQE--VVLVGGMTRMPK 381
		            P+   +  +   LE L + L    +     AL+      ASDI E  +VL GG   +  
		Sbjct: 245 VPRGFTLN-SNEILEALQEPLTG-IVSAVMVALEQCPPELASDISERGMVLTGGGALLRN 302
		
		Query: 382 VQEAVKKIFGREPHKGVNPDEVVALGAAI 410
		           +   + +  G       +P   VA G   
		Sbjct: 303 LDRLLMEETGIPVVVAEDPLTCVARGGGK 331
		
		
	179#RMA_0247	V8PROTEASE#V8 serine protease family signature.	53	1e-09
		>V8PROTEASE#V8 serine protease family signature.
		          Length = 336
		
		 Score = 52.7 bits (126), Expect = 1e-09
		 Identities = 40/196 (20%), Positives = 78/196 (39%), Gaps = 32/196 (16%)
		
		Query: 56  AVSAYDDTSSWTGTGFINDKNNGYIITNTHVVGGASIGTYFVTFY----------NGEQA 105
		            +     T ++  +G +  K+   ++TN HVV       + +  +          NG   
		Sbjct: 92  YIQVEAPTGTFIASGVVVGKDT--LLTNKHVVDATHGDPHALKAFPSAINQDNYPNGGFT 149
		
		Query: 106 EAKLIYYDIWQDYAVLKVE----SKDIPASATQISFA-SELPKLNQKVFVVGNTEAQGFS 160
		             ++  Y    D A++K      +K I       + + +   ++NQ + V G    +   
		Sbjct: 150 AEQITKYSGEGDLAIVKFSPNEQNKHIGEVVKPATMSNNAETQVNQNITVTGYPGDK--- 206
		
		Query: 161 FHTGYLSDLYNIAGLMPQC-TYVINL--NTTGGASGSPVLNDKIEAIGVLYGGGKTHSLA 217
		                ++ ++   G +       +    +TTGG SGSPV N+K E IG+ +GG   +   
		Sbjct: 207 ----PVATMWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVP-NEF- 260
		
		Query: 218 LHGDYVVRTLESLKNN 233
		              +  V   E+++N 
		Sbjct: 261 ---NGAVFINENVRNF 273
		
		
	193#RMA_0270	SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein s...	86	3e-20
		>SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein
		           signature.
		          Length = 347
		
		 Score = 85.6 bits (212), Expect = 3e-20
		 Identities = 63/359 (17%), Positives = 122/359 (33%), Gaps = 58/359 (16%)
		
		Query: 23  VGIDFGTTNSLIAIAANRKVKVIKSIDDKELIPTTIDFTSNNFTIGKNKGLRSIKRLFGK 82
		           + ID GT N+LI +     V    S+              +   +G +      K++ G+
		Sbjct: 13  LSIDLGTANTLIYVKGQGIVLNEPSVVAIR--QDRAGSPKSVAAVGHDA-----KQMLGR 65
		
		Query: 83  TLKEILNT-PALFSLVKDYLDVNSSELKLNFANKQLRVPEIAAEVFIYLKNQAEEQ-LKT 140
		           T   I    P    ++ D+                     +  ++  +   Q        
		Sbjct: 66  TPGNIAAIRPMKDGVIADF--------------------FVTEKMLQHFIKQVHSNSFMR 105
		
		Query: 141 NLTKAVITVPAHFNDAARGEVMLAAKIAGFEVLRLIAEPTAAAYAYGLNKNQKGCYLVYD 200
		              + ++ VP       R  +  +A+ AG   + LI EP AAA   GL  ++    +V D
		Sbjct: 106 PSPRVLVCVPVGATQVERRAIRESAQGAGAREVFLIEEPMAAAIGAGLPVSEATGSMVVD 165
		
		Query: 201 LGGGTFDVSILNIQEGIFQVIATNGDNMLGGNDIDVVITQYLCNKFDLPNSIDTLQLAKK 260
		           +GGGT +V++++        +  +    +GG+  D  I  Y+   +    S+     A++
		Sbjct: 166 IGGGTTEVAVIS-----LNGVVYSSSVRIGGDRFDEAIINYVRRNY---GSLIGEATAER 217
		
		Query: 261 AKETL-TYKDSFNNDNISINKQTLEQLILPLVERTINIAQECLEQAGNPNID-------- 311
		            K  + +         I +  + L + +        N   E L++     +         
		Sbjct: 218 IKHEIGSAYPGDEVREIEVRGRNLAEGVPRGFTLNSNEILEALQEPLTGIVSAVMVALEQ 277
		
		Query: 312 ------------GVILVGGATRIPLIKDELYKAFKIDILSDIDPDKAVVWGAALQAENL 358
		                       G++L GG   +  +   L +   I ++   DP   V  G     E +
		Sbjct: 278 CPPELASDISERGMVLTGGGALLRNLDRLLMEETGIPVVVAEDPLTCVARGGGKALEMI 336
		
		
RMA_0343	RMA_0366	Y	Y	N	RMA_0328	RMA_0367
	RMA_0343	-1	12	-3.259398	cell division protein ftsA
	RMA_0344	-3	11	-2.546686	membrane protease regulatory membrane protein
	RMA_0345	-1	12	-2.461549	cytochrome c
	RMA_0346	-1	13	-3.216663	hypothetical protein
	RMA_0347	-1	12	-3.059564	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine
	RMA_0348	-1	11	-2.795800	hypothetical protein
	RMA_0349	-1	12	-0.702478	ribonuclease E
	RMA_0350	-1	12	0.319999	cytochrome c oxidase assembly protein
	RMA_0351	-1	12	2.977129	ribosomal large subunit pseudouridine synthase
	RMA_0352	-1	13	3.698990	penicillin-binding protein 4*
	RMA_0353	1	16	5.100196	exodeoxyribonuclease III
	RMA_0354	0	16	5.248028	pyruvate dehydrogenase e1 component subunit
	RMA_0355	1	15	4.311599	pyruvate dehydrogenase subunit beta
	RMA_0356	2	14	2.551811	GTP-binding protein TypA
	RMA_0357	2	15	-0.241186	Outer membrane protein
	RMA_0358	2	16	1.084162	isocitrate dehydrogenase
	RMA_0359	3	16	1.604134	putative monovalent cation/H+ antiporter subunit
	RMA_0360	3	15	1.126280	putative monovalent cation/H+ antiporter subunit
	RMA_0361	2	15	2.560439	Heme exporter protein B
	RMA_0362	0	14	3.806121	hypothetical protein
	RMA_0363	0	15	2.613593	ubiquinol-cytochrome c reductase, iron-sulfur
	RMA_0364	0	14	0.853766	cytochrome b
	RMA_0365	-1	15	0.672754	endo/excinuclease amino terminal
	RMA_0366	-1	15	3.283876	cytochrome c1, heme protein
	249#RMA_0343	SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein s...	49	2e-08
		>SHAPEPROTEIN#Bacterial cell shape determinant MreB/Mbl protein
		           signature.
		          Length = 347
		
		 Score = 48.6 bits (116), Expect = 2e-08
		 Identities = 44/190 (23%), Positives = 77/190 (40%), Gaps = 35/190 (18%)
		
		Query: 188 ASAISCLTNDEKNLGSLIIDMGDKTTSFGIFFAGKLIYTGHVNIGSFHISSDI----AKV 243
		           A+AI       +  GS+++D+G  TT   +     ++Y+  V IG       I     + 
		Sbjct: 146 AAAIGAGLPVSEATGSMVVDIGGGTTEVAVISLNGVVYSSSVRIGGDRFDEAIINYVRRN 205
		
		Query: 244 FG--IDLVTAEKLKILYGNAMIPLFEKDSIINMEDFQVDTHHTLNTSVTIYKLAEVIRAR 301
		           +G  I   TAE++K   G+A    +  D +  +E    +    +    T+    E++ A 
		Sbjct: 206 YGSLIGEATAERIKHEIGSA----YPGDEVREIEVRGRNLAEGVPRGFTL-NSNEILEAL 260
		
		Query: 302 AEEILSMVKA------------EYDKATKGQVEVFRVVITGGGSQLRGLKELSNKIFEKQ 349
		            E +  +V A              D + +G      +V+TGGG+ LR L  L  +     
		Sbjct: 261 QEPLTGIVSAVMVALEQCPPELASDISERG------MVLTGGGALLRNLDRLLMEE---- 310
		
		Query: 350 SRIGKPEIIA 359
		              G P ++A
		Sbjct: 311 --TGIPVVVA 318
		
		
	251#RMA_0345	DHBDHDRGNASE#2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase sig...	27	0.032
		>DHBDHDRGNASE#2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
		           signature.
		          Length = 261
		
		 Score = 27.3 bits (60), Expect = 0.032
		 Identities = 9/14 (64%), Positives = 12/14 (85%)
		
		Query: 155 ISKPQDIADVILFL 168
		           ++KP DIAD +LFL
		Sbjct: 225 LAKPSDIADAVLFL 238
		
		
	262#RMA_0356	TCRTETOQM#Tetracycline resistance protein TetO/TetQ/TetM family ...	191	4e-55
		>TCRTETOQM#Tetracycline resistance protein TetO/TetQ/TetM family
		           signature.
		          Length = 639
		
		 Score =  191 bits (487), Expect = 4e-55
		 Identities = 105/457 (22%), Positives = 188/457 (41%), Gaps = 68/457 (14%)
		
		Query: 4   IRNIAIIAHVDHGKTTLVDNMLKQSGTFRANQAVAE--RAMDSNDLERERGITILAKCTA 61
		           I NI ++AHVD GKTTL +++L  SG      +V +     D+  LER+RGITI    T+
		Sbjct: 3   IINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITS 62
		
		Query: 62  LMWNDIRINIVDTPGHADFGGEVERILSMVDGVVLLVDASEGPMPQTKFVLSKALNLGLK 121
		             W + ++NI+DTPGH DF  EV R LS++DG +LL+ A +G   QT+ +      +G+ 
		Sbjct: 63  FQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIP 122
		
		Query: 122 PIVVINKIDRDDQRIKEVINEVFELFVA----------------------------LEAN 153
		            I  INKID++   +  V  ++ E   A                            +E N
		Sbjct: 123 TIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIEGN 182
		
		Query: 154 NDQL-----DFPIVYASGRAGRASLTFDDKINP------LDNLADDLAPLFDLIVQHVPK 202
		           +D L        +         +    +  + P       +N+   +  L ++I      
		Sbjct: 183 DDLLEKYMSGKSLEALELEQEESIRFHNCSLFPVYHGSAKNNIG--IDNLIEVITNKFYS 240
		
		Query: 203 PLADDKAPFSMLVTTREYNSFFGRVLTGRVQSGTVKINQNVKVLNRENKVLETGRITKIL 262
		                ++     V   EY+    R+   R+ SG + +  +V++  +E       +IT++ 
		Sbjct: 241 STHRGQSELCGKVFKIEYSEKRQRLAYIRLYSGVLHLRDSVRISEKEKI-----KITEMY 295
		
		Query: 263 AFRGLERIAINDATAGDIIAVAGVE---NANVADTICSPEVTEAVPSLPIDPPTLSMTFS 319
		                E   I+ A +G+I+ +       N+ + DT   P         P   P L  T  
		Sbjct: 296 TSINGELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLP--QRERIENP--LPLLQTTVE 351
		
		Query: 320 VNDSPLAGSEGTKVTSSLIGARLMREL-ESNVALKVTEAAEKNAFQVAGRGELQLGILIE 378
		            +       +   +  +L       E+ +S+  L+    +  +   ++  G++Q+ +   
		Sbjct: 352 PSKP----QQREMLLDAL------LEISDSDPLLRYYVDSATHEIILSFLGKVQMEVTCA 401
		
		Query: 379 TMRRE-GFELSISRPEVLFQTDEKGNKQEPMEEIQVD 414
		            ++ +   E+ I  P V++       K E    I+V 
		Sbjct: 402 LLQEKYHVEIEIKEPTVIYMERPLK-KAEYTIHIEVP 437
		
		
		
		 Score = 29.4 bits (66), Expect = 0.049
		 Identities = 14/80 (17%), Positives = 26/80 (32%), Gaps = 1/80 (1%)
		
		Query: 406 EPMEEIQVDVDDDYVGVVVKSLALRKAEMTDMRPSGGGKSRVTFIGPSRGLIGYHSQFLT 465
		           EP    ++    +Y+           A + D +     +  ++   P+R +  Y S    
		Sbjct: 537 EPYLSFKIYAPQEYLSRAYTDAPKYCANIVDTQ-LKNNEVILSGEIPARCIQEYRSDLTF 595
		
		Query: 466 ETRGTGIMNRIFHGYADYKG 485
		            T G  +      GY    G
		Sbjct: 596 FTNGRSVCLTELKGYHVTTG 615
		
		
	269#RMA_0363	PF07675#Cleaved Adhesin	29	0.010
		>PF07675#Cleaved Adhesin
		          Length = 1358
		
		 Score = 29.3 bits (65), Expect = 0.010
		 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
		
		Query: 54  DLSNIAVGQTVTVKWQGKPIFITNRTPDKIAEARAVKMSE 93
		           +L+  AVGQ VT+KW   P    N  P+         +SE
		Sbjct: 597 NLTGSAVGQKVTLKWSA-PNGTPNPNPNPNPNPGTTTLSE 635
		
		
RMA_0473	RMA_0506	Y	Y	N	RMA_0452	RMA_0504
	RMA_0473	2	11	-1.885089	dTDP-4-dehydrorhamnose reductase
	RMA_0474	1	11	-2.034042	putative nucleoside-diphosphate sugar epimerase
	RMA_0475	1	10	-2.869571	UDP-N-acetylglucosamine 2-epimerase
	RMA_0476	2	11	-3.923157	hypothetical protein
	RMA_0477	0	11	-2.959988	hypothetical protein
	RMA_0478	-1	11	-2.863676	glycosyltransferase
	RMA_0479	-1	13	-1.479769	RND family efflux transporter MFP subunit
	RMA_0480	-1	11	-1.466019	hypothetical protein
	RMA_0481	-2	11	-1.258214	putative hydrolase/acyltransferase
	RMA_0482	-2	10	-1.539228	glycosyltransferase
	RMA_0483	-2	9	-2.176576	ATPase components of ABC transporters
	RMA_0484	0	8	-3.608803	30S ribosomal protein S4
	RMA_0485	1	9	-3.973591	protoheme IX farnesyltransferase
	RMA_0487	1	9	-3.969334	hypothetical protein
	RMA_0488	1	8	-3.892925	Outer membrane assembly protein
	RMA_0489	-1	11	-4.101031	16S rRNA-processing protein RimM
	RMA_0490	-3	9	-1.498587	hypothetical protein
	RMA_0491	-1	15	3.304361	exodeoxyribonuclease VII small subunit
	RMA_0496	-2	16	4.337640	3-methyladenine DNA glycosylase
	RMA_0498	-1	17	4.185286	hypothetical protein
	RMA_0499	-2	14	3.082432	NADH dehydrogenase subunit E
	RMA_0501	-1	14	2.401332	NADH dehydrogenase subunit D
	RMA_0502	0	13	0.691332	NADH dehydrogenase subunit C
	RMA_0503	2	11	-1.445676	NADH dehydrogenase subunit B
	RMA_0504	4	11	-3.160399	NADH dehydrogenase subunit A
	RMA_0505	3	12	-2.756187	putative lipid A core - O-antigen ligase
	RMA_0506	1	12	-3.265879	hypothetical protein
	342#RMA_0474	NUCEPIMERASE#Nucleotide sugar epimerase signature.	54	3e-10
		>NUCEPIMERASE#Nucleotide sugar epimerase signature.
		          Length = 334
		
		 Score = 53.6 bits (129), Expect = 3e-10
		 Identities = 41/247 (16%), Positives = 87/247 (35%), Gaps = 38/247 (15%)
		
		Query: 7   TLMITGGTGSFGNAVLSRFLKS-------DIINDIKEIRIFSRDEKKQEDMRIAFNNPKL 59
		             ++TG  G  G  V  R L++       D +ND  ++ +       ++        P  
		Sbjct: 2   KYLVTGAAGFIGFHVSKRLLEAGHQVVGIDNLNDYYDVSL-------KQARLELLAQPGF 54
		
		Query: 60  KCYIGDVRNYKSIDE--AMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 117
		           + +  D+ + + + +  A    + VF +     V      P    ++N+ G  N+L    
		Sbjct: 55  QFHKIDLADREGMTDLFASGHFERVFISPHRLAVRYSLENPHAYADSNLTGFLNILEGCR 114
		
		Query: 118 NNKVTKVIVLST---------------DKAVYPINAMGLSKALMEKLAIAKARMRSPGET 162
		           +NK+  ++  S+               D   +P++    +K   E +A   + +     T
		Sbjct: 115 HNKIQHLLYASSSSVYGLNRKMPFSTDDSVDHPVSLYAATKKANELMAHTYSHLYGLPAT 174
		
		Query: 163 VLCVTRYGNVMASRGS---VIPLFINQIKQGKELTI-TEPSMTRFLMSLVDSVDLVLYAF 218
		            L   R+  V    G     +  F   + +GK + +     M R    + D  + ++   
		Sbjct: 175 GL---RFFTVYGPWGRPDMALFKFTKAMLEGKSIDVYNYGKMKRDFTYIDDIAEAIIRLQ 231
		
		Query: 219 EHGHQGD 225
		           +     D
		Sbjct: 232 DVIPHAD 238
		
		
	347#RMA_0479	RTXTOXIND#Gram-negative bacterial RTX secretion protein D signat...	32	0.002
		>RTXTOXIND#Gram-negative bacterial RTX secretion protein D
		           signature.
		          Length = 478
		
		 Score = 32.5 bits (74), Expect = 0.002
		 Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
		
		Query: 54  DNSRDYYANATGVVEQVSAHQGEIVKKGDILLVID--KNIAETTKSRAAALLNTKQEDYN 111
		             S++       +V+++   +GE V+KGD+LL +      A+T K++++ L    ++   
		Sbjct: 94  GRSKEIKPIENSIVKEIIVKEGESVRKGDVLLKLTALGAEADTLKTQSSLLQARLEQ--T 151
		
		Query: 112 RKEAL 116
		           R + L
		Sbjct: 152 RYQIL 156
		
		
RMA_0707	RMA_0770	Y	Y	Y	RMA_0687	RMA_0739
	RMA_0707	3	15	-1.178650	signal peptide peptidase SppA
	RMA_0708	5	18	-1.417766	integration host factor beta-subunit
	RMA_0713	4	20	-0.951598	integrase
	RMA_0714	3	21	-0.972271	Phage-associated protein
	RMA_0715	3	18	1.039014	putative toxin of toxin-antitoxin
	RMA_0716	3	21	0.833313	hypothetical protein
	RMA_0717	6	22	2.447884	conjugative transfer protein TraE
	RMA_0718	4	18	0.946873	hypothetical protein
	RMA_0719	5	18	1.692236	hypothetical protein
	RMA_0720	5	18	1.282659	F pilus assembly protein TraB
	RMA_0721	6	17	0.418856	conjugative transfer protein TraV
	RMA_0722	5	17	0.268877	conjugative transfer protein TraC
	RMA_0723	5	17	-0.686645	ATPase family protein
	RMA_0726	8	16	0.668073	conjugal DNA transfer protein TraU
	RMA_0727	10	16	-0.802259	conjugative transfer protein TrbC
	RMA_0728	9	14	-0.428628	conjugative transfer protein TraN
	RMA_0729	9	14	-0.485942	F pilus assembly protein TraF
	RMA_0730	9	12	-0.304521	F pilus assembly protein TraH
	RMA_0731	8	12	-0.504703	conjugative transfer protein TraG
	RMA_0732	7	13	-1.167129	hypothetical protein
	RMA_0733	7	15	-0.394316	putative conjugative transfer protein TraD
	RMA_0734	6	15	-0.578689	transposase
	RMA_0735	6	16	-0.334744	conjugal transfer protein TraA
	RMA_0736	6	21	-0.684348	transposase
	RMA_0739	8	21	-0.858387	hypothetical protein
	RMA_0740	7	18	0.153532	transposase
	RMA_0742	6	17	0.031426	transposase
	RMA_0745	5	16	-0.414094	transposase
	RMA_0746	6	21	-2.214857	transposase
	RMA_0747	6	21	-2.251632	transposase
	RMA_0748	6	22	-2.597082	transposase
	RMA_0749	6	22	-3.081665	transposase
	RMA_0750	6	22	-3.234891	transposase
	RMA_0751	6	21	-3.000251	DNA polymerase III subunit alpha
	RMA_0752	5	15	-2.333174	conjugal transfer protein TraD
	RMA_0753	4	13	-2.163580	guanosine polyphosphate
	RMA_0754	2	11	-0.926892	Signal transduction histidine kinase
	RMA_0755	2	12	-0.310258	site-specific DNA adenine methylase
	RMA_0756	0	11	1.224725	hypothetical protein
	RMA_0757	2	12	1.786712	*hypothetical protein
	RMA_0758	1	11	1.396262	cytidylate kinase
	RMA_0759	2	14	0.706700	30S ribosomal protein S1
	RMA_0760	-3	13	0.081772	ATP-dependent Clp protease proteolytic subunit
	RMA_0766	-1	13	-0.819411	*isopentenyl pyrophosphate isomerase
	RMA_0767	-1	14	-2.437150	putative acetyltransferase
	RMA_0769	0	15	-2.671483	acetyltransferase GNAT family protein
	RMA_0770	2	14	-1.975579	hypothetical protein
	513#RMA_0708	DNABINDINGHU#Prokaryotic integration host factor signature.	56	2e-14
		>DNABINDINGHU#Prokaryotic integration host factor signature.
		          Length = 91
		
		 Score = 56.2 bits (136), Expect = 2e-14
		 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
		
		Query: 2  MITKNYLIDKIHDKLNYLSKEDVKDSVDLILDYLNESLKEQKRIEIRNFGNFSIRKRK 59
		          M  K  LI K+ +    L+K+D   +VD +   ++  L + +++++  FGNF +R+R 
		Sbjct: 1  MANKQDLIAKVAEATE-LTKKDSAAAVDAVFSAVSSYLAKGEKVQLIGFGNFEVRERA 57
		
		
	530#RMA_0731	FLAGELLIN#Flagellin signature.	31	0.025
		>FLAGELLIN#Flagellin signature.
		          Length = 507
		
		 Score = 30.8 bits (69), Expect = 0.025
		 Identities = 35/261 (13%), Positives = 74/261 (28%), Gaps = 18/261 (6%)
		
		Query: 466 VASSIGTNIADNNLSIDNYSIGNRTIAQQNLTPTLQLAGGIIDDGGMRVTSTDNGRQVLT 525
		               + T+ A+NN ++D +     T              G I  G    T    G     
		Sbjct: 232 ANGQLTTDDAENNTAVDLFKTTKSTAGTAEAKAI----AGAIKGGKEGDTFDYKGVTFTI 287
		
		Query: 526 QAVDSLVNNYRSSKLLQDSYQSQFMSSQSYLDSLNDRYSDLTTTGNSIATEIGKRLSYEE 585
		                   N    K+       +   + + + +        T   +           +  
		Sbjct: 288 DTKTGNDGN---GKVSTTINGEKVTLTVADITAGAANVDAATLQSSKNVYTSVVNGQFTF 344
		
		Query: 586 AKSIGITDSQYLALQQMNSDSTSATDHTGSSNRKGTSTSATGSIGVNTMFGSGMTTVGSS 645
		                   ++   L+  N+    +      +     +     ++   TMF     +  S+
		Sbjct: 345 DDKTKNESAKLSDLEANNAVKGESKITVNGAEYTANAAGDKVTLAGKTMFIDKTASGVST 404
		
		Query: 646 NTLDQDQGKSVNQQQSY---NEALSKIKSATKD-----GRLSNANSNVQSLSNNLNSNFS 697
		              +       +        + ALSK+ +          R  +A +N+ +   NLNS  S
		Sbjct: 405 LINEDAAAAKKSTANPLASIDSALSKVDAVRSSLGAIQNRFDSAITNLGNTVTNLNSARS 464
		
		Query: 698 EQQSV--GQEIAQ-TKQNMQQ 715
		             +      E++  +K  + Q
		Sbjct: 465 RIEDADYATEVSNMSKAQILQ 485
		
		
	531#RMA_0732	SYCDCHAPRONE#Gram-negative bacterial type III secretion SycD cha...	48	6e-09
		>SYCDCHAPRONE#Gram-negative bacterial type III secretion SycD
		           chaperone signature.
		          Length = 168
		
		 Score = 48.4 bits (115), Expect = 6e-09
		 Identities = 16/97 (16%), Positives = 38/97 (39%)
		
		Query: 127 DFAEAYNNKGVSYKKLGKYQEAIRLYNIAIKYKPSFAEAYNNKGDTLNSLGKYQEAIENF 186
		           D  E   +   +  + GKY++A +++          +  +   G    ++G+Y  AI ++
		Sbjct: 34  DTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSY 93
		
		Query: 187 DLALKYAPRYPEAYYNKGISLINLGQHQEAIKNYDIS 223
		                   + P   ++    L+  G+  EA     ++
		Sbjct: 94  SYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLA 130
		
		
		
		 Score = 43.8 bits (103), Expect = 2e-07
		 Identities = 25/131 (19%), Positives = 46/131 (35%), Gaps = 3/131 (2%)
		
		Query: 224 LKYKPDYANAYYNKATSLMQLGKYQEAIKNFDSVIKYQCDNEDAYNLKGCIFSILGKQQE 283
		            +   D     Y+ A +  Q GKY++A K F ++      +   +   G     +G+   
		Sbjct: 29  NEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDL 88
		
		Query: 284 AIKNYDLAIKYKPNFAAAYCNKGTSFRKLGKYQDAIKSYDLA---IKYKSDYAESYLEKG 340
		           AI +Y               +      + G+  +A     LA   I  K+++ E      
		Sbjct: 89  AIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKTEFKELSTRVS 148
		
		Query: 341 IVLVNLGKYKE 351
		            +L  +   KE
		Sbjct: 149 SMLEAIKLKKE 159
		
		
		
		 Score = 42.2 bits (99), Expect = 7e-07
		 Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 3/106 (2%)
		
		Query: 62  EEYFNIGRSLYKLGKYKKAIKNYDLAIKYKTDCAKCYNNKGRALNELANHQEAITNYDLA 121
		           E+ +++  + Y+ GKY+ A K +          ++ +   G     +  +  AI +Y   
		Sbjct: 37  EQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYG 96
		
		Query: 122 IKYDIDFAEAYNNKGVSYKKLGKYQEAIRLYNIA---IKYKPSFAE 164
		              DI       +      + G+  EA     +A   I  K  F E
		Sbjct: 97  AIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKTEFKE 142
		
		
		
		 Score = 41.1 bits (96), Expect = 2e-06
		 Identities = 18/95 (18%), Positives = 30/95 (31%)
		
		Query: 164 EAYNNKGDTLNSLGKYQEAIENFDLALKYAPRYPEAYYNKGISLINLGQHQEAIKNYDIS 223
		           E   +        GKY++A + F             +   G     +GQ+  AI +Y   
		Sbjct: 37  EQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYG 96
		
		Query: 224 LKYKPDYANAYYNKATSLMQLGKYQEAIKNFDSVI 258
		                      ++ A  L+Q G+  EA        
		Sbjct: 97  AIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQ 131
		
		
		
		 Score = 35.3 bits (81), Expect = 2e-04
		 Identities = 23/131 (17%), Positives = 43/131 (32%), Gaps = 10/131 (7%)
		
		Query: 178 KYQEAIENF-----DLA--LKYAPRYPEAYYNKGISLINLGQHQEAIKNYDISLKYKPDY 230
		           +YQ A+E+F      +A   + +    E  Y+   +    G++++A K +          
		Sbjct: 10  EYQLAMESFLKGGGTIAMLNEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYD 69
		
		Query: 231 ANAYYNKATSLMQLGKYQEAIKNFDSVIKYQCDNEDAYNLKGCIFSILGKQQEAIKNYDL 290
		           +  +         +G+Y  AI ++                        G+  EA     L
		Sbjct: 70  SRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFL 129
		
		Query: 291 A---IKYKPNF 298
		           A   I  K  F
		Sbjct: 130 AQELIADKTEF 140
		
		
		
		 Score = 34.5 bits (79), Expect = 3e-04
		 Identities = 15/87 (17%), Positives = 28/87 (32%)
		
		Query: 112 QEAITNYDLAIKYDIDFAEAYNNKGVSYKKLGKYQEAIRLYNIAIKYKPSFAEAYNNKGD 171
		           ++A   +      D   +  +   G   + +G+Y  AI  Y+              +  +
		Sbjct: 53  EDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAE 112
		
		Query: 172 TLNSLGKYQEAIENFDLALKYAPRYPE 198
		            L   G+  EA     LA +      E
		Sbjct: 113 CLLQKGELAEAESGLFLAQELIADKTE 139
		
		
		
		 Score = 33.7 bits (77), Expect = 6e-04
		 Identities = 20/97 (20%), Positives = 32/97 (32%), Gaps = 1/97 (1%)
		
		Query: 263 DNEDAYNLKGCIFSILGKQQEAIKNYDLAIKYKPNFAAAYCNKGTSFRKLGKYQDAIKSY 322
		             E  Y+L        GK ++A K +          +  +   G   + +G+Y  AI SY
		Sbjct: 35  TLEQLYSL-AFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSY 93
		
		Query: 323 DLAIKYKSDYAESYLEKGIVLVNLGKYKEAKENFNLA 359
		                               L+  G+  EA+    LA
		Sbjct: 94  SYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLA 130
		
		
		
		 Score = 28.7 bits (64), Expect = 0.024
		 Identities = 15/86 (17%), Positives = 28/86 (32%)
		
		Query: 304 NKGTSFRKLGKYQDAIKSYDLAIKYKSDYAESYLEKGIVLVNLGKYKEAKENFNLAFKYK 363
		           +   +  + GKY+DA K +          +  +L  G     +G+Y  A  +++      
		Sbjct: 41  SLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMD 100
		
		Query: 364 SNLIEEYEAIIKALRQLGNDLMANEF 389
		                      + L Q G    A   
		Sbjct: 101 IKEPRFPFHAAECLLQKGELAEAESG 126
		
		
	533#RMA_0734	FLGFLIH#Flagellar assembly protein FliH signature.	35	3e-04
		>FLGFLIH#Flagellar assembly protein FliH signature.
		          Length = 228
		
		 Score = 34.8 bits (79), Expect = 3e-04
		 Identities = 16/38 (42%), Positives = 25/38 (65%)
		
		Query: 277 EGLQVGKAQGIQIGEAKGIQIGEAKGIQIGKAEGKAEE 314
		           +G Q G A+G Q G  +G Q G A+G++ G AE K+++
		Sbjct: 54  QGYQAGIAEGRQQGHKQGYQEGLAQGLEQGLAEAKSQQ 91
		
		
		
		 Score = 32.8 bits (74), Expect = 0.001
		 Identities = 15/36 (41%), Positives = 22/36 (61%)
		
		Query: 267 QQEGKELGILEGLQVGKAQGIQIGEAKGIQIGEAKG 302
		            ++G + GI EG Q G  QG Q G A+G++ G A+ 
		Sbjct: 52  HEQGYQAGIAEGRQQGHKQGYQEGLAQGLEQGLAEA 87
		
		
	537#RMA_0740	HTHFIS#FIS bacterial regulatory protein HTH signature.	28	0.035
		>HTHFIS#FIS bacterial regulatory protein HTH signature.
		          Length = 484
		
		 Score = 28.3 bits (63), Expect = 0.035
		 Identities = 9/22 (40%), Positives = 12/22 (54%)
		
		Query: 103 NLLIFGPSGVGKSHLAAAIGYA 124
		            L+I G SG GK  +A A+   
		Sbjct: 162 TLMITGESGTGKELVARALHDY 183
		
		
	539#RMA_0745	HTHFIS#FIS bacterial regulatory protein HTH signature.	28	0.007
		>HTHFIS#FIS bacterial regulatory protein HTH signature.
		          Length = 484
		
		 Score = 27.9 bits (62), Expect = 0.007
		 Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
		
		Query: 18  AEFKESAIKLAIE-SKQPVAQTARELGITKSSLYNWVNKY 56
		           AE +   I  A+  ++    + A  LG+ +++L   + + 
		Sbjct: 434 AEMEYPLILAALTATRGNQIKAADLLGLNRNTLRKKIREL 473
		
		
	557#RMA_0769	SACTRNSFRASE#Streptothricin acetyltransferase signature.	36	2e-05
		>SACTRNSFRASE#Streptothricin acetyltransferase signature.
		          Length = 173
		
		 Score = 35.7 bits (82), Expect = 2e-05
		 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
		
		Query: 42  FINREGYGVALASLDNTIVGFIAWSKSLLFVSDKTRIHIEVLVIDENYRGKQIGKKLMEY 101
		           ++  EG    L  L+N  +G I    +           IE + + ++YR K +G  L+  
		Sbjct: 59  YVEEEGKAAFLYYLENNCIGRIKIRSNW-----NGYALIEDIAVAKDYRKKGVGTALLHK 113
		
		Query: 102 LEEIAK 107
		             E AK
		Sbjct: 114 AIEWAK 119
		
		
RMA_0849	RMA_0862	Y	Y	N	RMA_0823	RMA_0891
	RMA_0849	3	9	-0.164072	hypothetical protein
	RMA_0850	3	8	-0.492343	DNA repair protein RecO
	RMA_0851	2	8	-0.290658	putative glycoprotein endopeptidase
	RMA_0852	2	9	-0.310691	hypothetical protein
	RMA_0853	2	8	1.640055	translation initiation factor IF-2
	RMA_0854	1	12	0.510313	transcription elongation factor NusA
	RMA_0855	1	12	0.043428	hypothetical protein
	RMA_0856	0	14	-0.189181	hypothetical protein
	RMA_0859	3	12	0.790711	hemolysin A
	RMA_0860	5	16	1.532360	tyrosyl-tRNA synthetase
	RMA_0861	6	17	-1.020361	hypothetical protein
	RMA_0862	6	20	-0.591752	hypothetical protein
	610#RMA_0853	TCRTETOQM#Tetracycline resistance protein TetO/TetQ/TetM family ...	64	9e-13
		>TCRTETOQM#Tetracycline resistance protein TetO/TetQ/TetM family
		           signature.
		          Length = 639
		
		 Score = 64.5 bits (157), Expect = 9e-13
		 Identities = 44/134 (32%), Positives = 62/134 (46%), Gaps = 19/134 (14%)
		
		Query: 336 VMGHVDHGKTSLLDALKSTDIAAGELG------------------GITQHIGAYRVTLAD 377
		           V+ HVD GKT+L ++L     A  ELG                  GIT   G       +
		Sbjct: 8   VLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITSFQWEN 67
		
		Query: 378 GRAITFIDTPGHEAFSEMRSRGAKVTDIVIIVVAADDGIKTQTVEAINHAKAAGVPIIVA 437
		            + +  IDTPGH  F     R   V D  I++++A DG++ QT    +  +  G+P I  
		Sbjct: 68  TK-VNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFF 126
		
		Query: 438 INKIDKPDIDIERV 451
		           INKID+  ID+  V
		Sbjct: 127 INKIDQNGIDLSTV 140
		
		
RMA_1111	RMA_1118	Y	Y	N	RMA_1082	RMA_1149
	RMA_1111	3	14	1.669488	lipoprotein releasing system, transmembrane
	RMA_1112	4	15	1.738501	lipoprotein releasing system ATP-binding protein
	RMA_1113	4	15	1.748115	hypothetical protein
	RMA_1114	4	16	2.641706	hemolysin-like protein
	RMA_1115	5	17	2.815689	cytochrome c-type biogenesis protein ccmF
	RMA_1118	6	19	3.411724	outer membrane protein OmpB
	782#RMA_1118	VACCYTOTOXIN#Helicobacter pylori vacuolating cytotoxin signature.	32	0.034
		>VACCYTOTOXIN#Helicobacter pylori vacuolating cytotoxin signature.
		          Length = 1291
		
		 Score = 31.5 bits (71), Expect = 0.034
		 Identities = 64/289 (22%), Positives = 95/289 (32%), Gaps = 59/289 (20%)
		
		Query: 419 TGNFTGDASNPGNTAGVITFAANGTLASA-----SADANVAVTNNITAIEASGV---GVV 470
		           T   TG+ +    T G    A  G +AS      + D   +   NI A    G       
		Sbjct: 278 TSKVTGEVNFNHLTVGDHNAAQAGIIASNKTHIGTLDLWQSAGLNIIAPPEGGYKDKPND 337
		
		Query: 471 QLSGTHTAELRLGNAGSVFQLADGTVINGKVNQ-------TAVVGGALAAGAITLDGSAT 523
		           + S T     +     S    ++  VIN   +        T V+ G  A G  T+     
		Sbjct: 338 KPSNTTQNNAKNDKQESSQNNSNTQVINPPNSAQKTEIQPTQVIDGPFAGGKNTVVNINR 397
		
		Query: 524 IT----GDIGNGGGAAAL-----------QGITLANDA----------TKTLTLGGANII 558
		           I     G I  GG  A+L            GI L+N A          T  +T+ G   +
		Sbjct: 398 INTNADGTIRVGGFKASLTTNAAHLHIGKGGINLSNQASGRSLLVENLTGNITVDGPLRV 457
		
		Query: 559 GSNVGG-TIDFQANGGTIKLTSTQNNILVDFDLDITTDQTGVVDASSLTNA--------- 608
		            + VGG  +   +     K  +   N    F+ DI+  +   +   + T           
		Sbjct: 458 NNQVGGYALAGSSANFEFKAGTDTKNGTATFNNDISLGRFVNLKVDAHTANFKGIDTGNG 517
		
		Query: 609 --QTLTISGTIGTIGANNKTLGQFNIGSSKTALNGGNVAINELVIGNNG 655
		              TL  SG    +  N          ++ T +   N  INELV+  NG
		Sbjct: 518 GFNTLDFSGVTNKVNINKLI-------TASTNVAVKNFNINELVVKTNG 559
		
		
		
		 Score = 31.5 bits (71), Expect = 0.041
		 Identities = 40/165 (24%), Positives = 61/165 (36%), Gaps = 18/165 (10%)
		
		Query: 143 NAQAAATKNAQNVVAPFNGGAA----IANNDLSGVGTIDWGAADSTLVFNLANPTTQKAP 198
		           +AQ    +  Q +  PF GG      I   + +  GTI  G   ++L  N A+    K  
		Sbjct: 369 SAQKTEIQPTQVIDGPFAGGKNTVVNINRINTNADGTIRVGGFKASLTTNAAHLHIGKGG 428
		
		Query: 199 LVLGNNA----VIANGVNGTL---------NVTNGFIQVSDKSFATVKAINIGDGQGFIF 245
		           + L N A    ++   + G +         N   G+      +    KA          F
		Sbjct: 429 INLSNQASGRSLLVENLTGNITVDGPLRVNNQVGGYALAGSSANFEFKAGTDTKNGTATF 488
		
		Query: 246 NTDATVGNALNLQAGGATINFNGTD-GTGRLVLLSKNGAATDFNV 289
		           N D ++G  +NL+    T NF G D G G    L  +G     N+
		Sbjct: 489 NNDISLGRFVNLKVDAHTANFKGIDTGNGGFNTLDFSGVTNKVNI 533
		
		
RMA_1229	RMA_1252	Y	Y	N	RMA_1207	RMA_1255
	RMA_1229	-1	10	-3.447469	UDP-glucose 6-dehydrogenase
	RMA_1230	-1	7	-1.699019	hypothetical protein
	RMA_1231	0	7	-0.966493	AmpG protein
	RMA_1232	0	8	-1.270213	Sec-independent protein translocase protein
	RMA_1233	0	9	-0.750235	seryl-tRNA synthetase
	RMA_1234	0	9	-1.015764	VirB4
	RMA_1235	1	10	0.250265	hypothetical protein
	RMA_1236	2	11	-0.705445	tellurium resistance protein TerC
	RMA_1237	2	11	0.103632	hypothetical protein
	RMA_1238	2	14	0.502274	putative methyltransferase
	RMA_1241	5	16	1.039806	NADH dehydrogenase subunit J
	RMA_1242	3	17	1.887577	NADH dehydrogenase subunit K
	RMA_1243	1	13	2.687642	NADH dehydrogenase subunit L
	RMA_1244	-1	12	2.750752	NADH dehydrogenase subunit M
	RMA_1245	-2	12	3.671327	cytochrome c biogenesis protein CcmA
	RMA_1246	-1	12	3.838442	NADH dehydrogenase subunit I
	RMA_1247	0	13	4.516778	NADH dehydrogenase subunit H
	RMA_1248	0	13	3.741160	NADH dehydrogenase subunit G
	RMA_1249	0	14	4.119973	hypothetical protein
	RMA_1250	-1	13	3.426551	aconitate hydratase
	RMA_1251	-1	12	3.090405	F0F1 ATP synthase subunit epsilon
	RMA_1252	0	12	3.163793	F0F1 ATP synthase subunit beta
	858#RMA_1231	TCRTETB#Tetracycline resistance protein TetB signature.	34	0.002
		>TCRTETB#Tetracycline resistance protein TetB signature.
		          Length = 458
		
		 Score = 34.1 bits (78), Expect = 0.002
		 Identities = 32/183 (17%), Positives = 78/183 (42%), Gaps = 8/183 (4%)
		
		Query: 381 LLLIILFIFLYKAADSIPMAMSSP-LFLDLSFTTHEIAVIYKAYGLLIMIVGGALGGVLA 439
		           +L+ +  +  +   + + + +S P +  D +        +  A+ +L   +G A+ G L+
		Sbjct: 15  ILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAF-MLTFSIGTAVYGKLS 73
		
		Query: 440 AKMGIFHSVLIGGVIQLLSPLMFMILATIGYDIKPF-ILTVTVQNFCAGFAGTIISIYFA 498
		            ++GI   +L G +I         ++  +G+      I+   +Q   A     ++ +  A
		Sbjct: 74  DQLGIKRLLLFGIIINCFGS----VIGFVGHSFFSLLIMARFIQGAGAAAFPALVMVVVA 129
		
		Query: 499 SLCNSEFVATQYSIIASFSSLSRIILASLGGICAKYLTWPVFFLGNTLFSMLFIPIFYKI 558
		                E     + +I S  ++   +  ++GG+ A Y+ W    L   + +++ +P   K+
		Sbjct: 130 RYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMI-TIITVPFLMKL 188
		
		Query: 559 YRK 561
		            +K
		Sbjct: 189 LKK 191
		
		
	861#RMA_1234	BONTOXILYSIN#Bontoxilysin signature.	30	0.046
		>BONTOXILYSIN#Bontoxilysin signature.
		          Length = 1196
		
		 Score = 30.3 bits (68), Expect = 0.046
		 Identities = 8/51 (15%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
		
		Query: 132 KVNIKNFNSLINSLSNKLITDFENNYLDSAFQKLDNITNNILNDLNEFGAE 182
		            ++I++  +  NS   +++ +  + Y    F       +NI+ D++     
		Sbjct: 810 FLDIQSIKNFFNSQVEQVMKEILSPYQLLLFASKGP-NSNIIEDISGKNTL 859
		
		
RMA_1268	RMA_1308	Y	Y	Y	RMA_1247	RMA_1315
	RMA_1268	5	15	-2.402290	Iojap-related protein
	RMA_1269	3	14	-2.205370	BolA-like protein
	RMA_1270	1	15	-1.672692	transposase
	RMA_1283	-2	11	0.538708	*translation initiation factor IF-1
	RMA_1284	-2	9	-0.863666	Maf-like protein
	RMA_1285	2	12	2.786489	DnaK suppressor-like protein
	RMA_1286	2	11	2.732954	site-specific tyrosine recombinase XerC
	RMA_1289	1	10	3.519576	phospholipase D superfamily protein PLD
	RMA_1294	2	10	3.788082	UbiD family decarboxylase
	RMA_1295	2	10	3.309010	parvulin-like peptidyl-prolyl isomerase
	RMA_1296	4	12	4.098785	outer membrane protein OmpA
	RMA_1297	-1	12	1.541948	ankyrin repeat-containing protein
	RMA_1298	0	13	1.789900	cell division protein FtsK
	RMA_1301	3	14	0.074855	methionine aminopeptidase
	RMA_1305	3	14	-0.811331	undecaprenyl-phosphate
	RMA_1306	2	15	-0.110100	hypothetical protein
	RMA_1307	2	14	-0.178246	hypothetical protein
	RMA_1308	2	12	1.325713	putative outer surface protein
	897#RMA_1296	FLAGELLIN#Flagellin signature.	37	7e-04
		>FLAGELLIN#Flagellin signature.
		          Length = 507
		
		 Score = 37.3 bits (86), Expect = 7e-04
		 Identities = 31/290 (10%), Positives = 62/290 (21%), Gaps = 1/290 (0%)
		
		Query: 353 LNGALSQVTGNIGNTNSLATISIGAGTATLGGAVIKATTIDLTDAASVLTLTNANA-VLT 411
		           L+           N     TI +        G                L  +  N     
		Sbjct: 137 LSQDNQMKIQVGANDGETITIDLQKIDVKSLGLDGFNVNGPKEATVGDLKSSFKNVTGYD 196
		
		Query: 412 GAIDNTTGVDNVGVLNLNGALSQVTGNIGNTNSLATISVGAGTATLGGAVIKATTTDLTD 471
		                                +            A               +    T  + 
		Sbjct: 197 TYAVGANKYRVDVNSGAVVTDTTAPTVPDKVYVNAANGQLTTDDAENNTAVDLFKTTKST 256
		
		Query: 472 AASVLTLTNANAVLTGAIDNTTGVDNVGVLNLNGALSQVTGNIGNTNSLATISIGAGTAT 531
		           A +      A A+  G   +T     V         +   G +  T +   +++     T
		Sbjct: 257 AGTAEAKAIAGAIKGGKEGDTFDYKGVTFTIDTKTGNDGNGKVSTTINGEKVTLTVADIT 316
		
		Query: 532 LGGAVIKATTTDLTDAASVLTLTNANAVLTGAIDNTKGVDNVGVLNLNGALSQVTGNIGN 591
		            G A + A T   +       +           + +  + ++   N     S++T N   
		Sbjct: 317 AGAANVDAATLQSSKNVYTSVVNGQFTFDDKTKNESAKLSDLEANNAVKGESKITVNGAE 376
		
		Query: 592 TNSLATISVGAGTATLGGAVIKATTIDLTDAASVLTLTNANAVLTGAIDN 641
		             + A                 A+ +             + A    +ID+
		Sbjct: 377 YTANAAGDKVTLAGKTMFIDKTASGVSTLINEDAAAAKKSTANPLASIDS 426
		
		
		
		 Score = 35.4 bits (81), Expect = 0.002
		 Identities = 44/295 (14%), Positives = 67/295 (22%), Gaps = 5/295 (1%)
		
		Query: 503 LNGALSQVTGNIGNTNSLATISIGAGTATLGGAVIKATTTDLTDAASVLTLTNANAVLTG 562
		           L+           N     TI +        G                L  +  N     
		Sbjct: 137 LSQDNQMKIQVGANDGETITIDLQKIDVKSLGLDGFNVNGPKEATVGDLKSSFKNVTGYD 196
		
		Query: 563 AIDNTKGVDNVGVLNLNGALSQVTGNIGNTNSLATISVGAGTATLGGAVIKATTIDLTDA 622
		                     V V     + + VT     T         A            T +DL   
		Sbjct: 197 TYAVGANKYRVDV----NSGAVVTDTTAPTVPDKVYVNAANGQLTTDDAENNTAVDLFKT 252
		
		Query: 623 ASVLTLTNANAVLTGAIDNTTGVDNVGVLNLNGALSQVTGNIGNTNSLATISVGAGTATL 682
		                 T     + GAI      D      +   +   TGN GN     TI+ G      
		Sbjct: 253 TKSTAGTAEAKAIAGAIKGGKEGDTFDYKGVTFTIDTKTGNDGNGKVSTTIN-GEKVTLT 311
		
		Query: 683 GGAVIKATTIDLTDAASVLTLTNANAVLTGAIDNTKGVDNVGVLNLNGALSQVTGNIGNT 742
		              +                    + V      + K  +    L+   A + V G    T
		Sbjct: 312 VADITAGAANVDAATLQSSKNVYTSVVNGQFTFDDKTKNESAKLSDLEANNAVKGESKIT 371
		
		Query: 743 NSLATISIGAGTATLGGAVIKATTIDLTDAASVLTLTNANAVLTGAIDNTTGVDN 797
		            + A  +  A    +  A             S L   +A A      +    +D+
		Sbjct: 372 VNGAEYTANAAGDKVTLAGKTMFIDKTASGVSTLINEDAAAAKKSTANPLASIDS 426
		
		
	903#RMA_1307	56KDTSANTIGN#Rickettsia 56kDa type-specific antigen protein sign...	31	0.005
		>56KDTSANTIGN#Rickettsia 56kDa type-specific antigen protein
		           signature.
		          Length = 533
		
		 Score = 30.7 bits (69), Expect = 0.005
		 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 13/71 (18%)
		
		Query: 131 YVDFVDLSMFKVFTGAGVG-AAFIKEKINSKDIKDGVTKTFNGTTKNKTNFAYQLSLGTS 189
		           Y D V    F ++ G G G  ++   KI++KD+            K  T      +LG +
		Sbjct: 445 YADLVTTESFSIYGGVGAGLGSYTYAKIDNKDV------------KGYTGMVASGALGVA 492
		
		Query: 190 FEVAQGVKAEL 200
		              A+GV  +L
		Sbjct: 493 INAAEGVCVDL 503
		
		
	904#RMA_1308	OUTRMMBRANEA#Outer membrane protein A signature.	41	2e-06
		>OUTRMMBRANEA#Outer membrane protein A signature.
		          Length = 346
		
		 Score = 40.7 bits (95), Expect = 2e-06
		 Identities = 33/187 (17%), Positives = 60/187 (32%), Gaps = 21/187 (11%)
		
		Query: 6   KLLLIAATSATILSSSLSFAEGMDNEWYLRIDTGAAMFNEEKDKATGVKLKSNTTVPVDL 65
		           K   IA   A    ++++ A   DN WY     G + +++            N       
		Sbjct: 2   KKTAIAIAVALAGFATVAQAAPKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAF 61
		
		Query: 66  GIGYYISENCRADLTLGTIIGGKLKKSGAATNAPFTGTNVSASHKPTITRLLINGYVDLT 125
		           G GY ++     +  +G    G++   G+  N  +    V  + K               
		Sbjct: 62  G-GYQVNPYVGFE--MGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPIT--------- 109
		
		Query: 126 NFDMFDVFAGAGVGPALVKEKITYNGITGLSSNTKNRTNISYKLTLGTSAQIADGVKVEL 185
		             D  D++   G     V    T + + G + +T     +S     G    I   +   L
		Sbjct: 110 --DDLDIYTRLGGM---VWRADTKSNVYGKNHDTG----VSPVFAGGVEYAITPEIATRL 160
		
		Query: 186 AYSWIDD 192
		            Y W ++
		Sbjct: 161 EYQWTNN 167
		
		
RMA_0005	RMA_0020	N	Y	Y	RMA_0001	RMA_0079
	RMA_0005	-1	8	0.192447	putative bifunctional glutamate synthase subunit
	RMA_0006	-1	12	0.076476	UDP-N-acetylglucosamine acyltransferase
	RMA_0007	1	11	0.311664	(3R)-hydroxymyristoyl-ACP dehydratase
	RMA_0008	2	11	0.012603	UDP-3-O-[3-hydroxymyristoyl] glucosamine
	RMA_0017	4	11	-0.611330	*putative P-loop hydrolase
	RMA_0018	4	11	-0.292554	Zinc/manganese ABC transporter substrate binding
	RMA_0019	3	11	-0.263372	Poly(A) polymerase
	RMA_0020	4	11	0.171612	cell surface antigen Sca1
	5#RMA_0005	NUCEPIMERASE#Nucleotide sugar epimerase signature.	33	0.007
		>NUCEPIMERASE#Nucleotide sugar epimerase signature.
		          Length = 334
		
		 Score = 32.8 bits (75), Expect = 0.007
		 Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
		
		Query: 383 NILVTGL-GPAGFSLSYYLLRSGHNVVAIDGL 413
		             LVTG  G  GF +S  LL +GH VV ID L
		Sbjct: 2   KYLVTGAAGFIGFHVSKRLLEAGHQVVGIDNL 33
		
		
	6#RMA_0006	TYPE4SSCAGA#Type IV secretion system CagA exotoxin signature.	29	0.033
		>TYPE4SSCAGA#Type IV secretion system CagA exotoxin signature.
		          Length = 1147
		
		 Score = 28.5 bits (63), Expect = 0.033
		 Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 25/99 (25%)
		
		Query: 49  IEGITEIGENTVIYPFSSIGQPPQILKYANERSSTIIGSNNTIR-EYVTVQAGSQGG--- 104
		           +EG+ +I  N   Y F+      Q+L + N  SS ++GS+N I  E V++  G  GG   
		Sbjct: 277 VEGVADIDPN---YKFN------QLLIHNNALSSVLMGSHNGIEPEKVSLLYGGNGGPGA 327
		
		Query: 105 --------GMVTRVGNNNLFMVGVHIGHDCKIGNNVVFA 135
		                   G   + GNN   ++ VH+    K G+ +V A
		Sbjct: 328 RHDWNATVGYKDQQGNNVATIINVHM----KNGSGLVIA 362
		
		
	10#RMA_0018	ADHESNFAMILY#Adhesin family signature.	95	2e-24
		>ADHESNFAMILY#Adhesin family signature.
		          Length = 309
		
		 Score = 94.5 bits (235), Expect = 2e-24
		 Identities = 53/250 (21%), Positives = 102/250 (40%), Gaps = 27/250 (10%)
		
		Query: 51  KQAFAGMMTYLALLFLTFLSL-----TSYAKPKIVVSITPIGSIVSMLVKDKADIESLAI 105
		           K+    ++ +L+ + L   +      TS  K K+V + + I  I   +  DK D+ S+  
		Sbjct: 2   KKLGTLLVLFLSAIILVACASGKKDTTSGQKLKVVATNSIIADITKNIAGDKIDLHSIVP 61
		
		Query: 106 SSDCPHHYNLKPSDLVKVKNSDIAIYI--------NEQFDGFAEKLIDNYSKNIIKISDI 157
		               PH Y   P D+ K   +D+  Y         N  F    E      +K+   +SD 
		Sbjct: 62  IGQDPHEYEPLPEDVKKTSEADLIFYNGINLETGGNAWFTKLVENAKKTENKDYFAVSDG 121
		
		Query: 158 KSLTTI-------KDNWHIWLDLNNAVILLQEFARIFSENFPELQEDINNNLSTALKELN 210
		             +  +       K++ H WL+L N +I  +  A+  S   P  +E    NL     +L+
		Sbjct: 122 VDVIYLEGQNEKGKEDPHAWLNLENGIIFAKNIAKQLSAKDPNNKEFYEKNLKEYTDKLD 181
		
		Query: 211 KLQEIKNNELATI----KDVILLSDSSEYFFLNTNIKTAKLY---SESQTSLRYISKLED 263
		           KL +   ++   I    K ++    + +YF     + +A ++   +E + +   I  L +
		Sbjct: 182 KLDKESKDKFNKIPAEKKLIVTSEGAFKYFSKAYGVPSAYIWEINTEEEGTPEQIKTLVE 241
		
		Query: 264 LIKESNNKCL 273
		            ++++    L
		Sbjct: 242 KLRQTKVPSL 251
		
		
	12#RMA_0020	GPOSANCHOR#Gram-positive coccus surface protein anchor signature.	32	0.018
		>GPOSANCHOR#Gram-positive coccus surface protein anchor signature.
		          Length = 539
		
		 Score = 32.3 bits (73), Expect = 0.018
		 Identities = 19/157 (12%), Positives = 48/157 (30%), Gaps = 4/157 (2%)
		
		Query: 321 TKNTKSLQKLYMQLTSAQKTIETLKSKAEKIETQIKVGGEDKNKIKKLEKKLTSKNNKAD 380
		                   +L   L  A        +K + +E +       K  ++K  +   + +    
		Sbjct: 186 AALEARQAELEKALEGAMNFSTADSAKIKTLEAEKAALAARKADLEKALEGAMNFSTADS 245
		
		Query: 381 RLFQKIEK--IDIPANKISIESQETVPVTTASTQVSAFQAQQARINEAQQGVLVQKNQQH 438
		              + +E     + A +  +E      +  ++   +  +  +A     +        +  
		Sbjct: 246 AKIKTLEAEKAALEARQAELEKALEGAMNFSTADSAKIKTLEAEKAALEA--EKADLEHQ 303
		
		Query: 439 IAAEKTKKQRQAEDKQRTEREKKKQEAQKQLSEIKKQ 475
		                  +Q    D   +   KK+ EA+ Q  E + +
		Sbjct: 304 SQVLNANRQSLRRDLDASREAKKQLEAEHQKLEEQNK 340
		
		
		
		 Score = 32.0 bits (72), Expect = 0.026
		 Identities = 21/193 (10%), Positives = 51/193 (26%)
		
		Query: 324 TKSLQKLYMQLTSAQKTIETLKSKAEKIETQIKVGGEDKNKIKKLEKKLTSKNNKADRLF 383
		                 L  +    +K +E   + +     +IK    +K  ++  + +L      A    
		Sbjct: 147 EAEKAALAARKADLEKALEGAMNFSTADSAKIKTLEAEKAALEARQAELEKALEGAMNFS 206
		
		Query: 384 QKIEKIDIPANKISIESQETVPVTTASTQVSAFQAQQARINEAQQGVLVQKNQQHIAAEK 443
		                                     + + +   +                 +   A  +
		Sbjct: 207 TADSAKIKTLEAEKAALAARKADLEKALEGAMNFSTADSAKIKTLEAEKAALEARQAELE 266
		
		Query: 444 TKKQRQAEDKQRTEREKKKQEAQKQLSEIKKQEQAIKTAADKAKEVAASAKKETSRTALR 503
		              +           + K  EA+K   E +K +   ++    A   +     + SR A +
		Sbjct: 267 KALEGAMNFSTADSAKIKTLEAEKAALEAEKADLEHQSQVLNANRQSLRRDLDASREAKK 326
		
		Query: 504 TMQDKMNGYSEQL 516
		            ++ +     EQ 
		Sbjct: 327 QLEAEHQKLEEQN 339
		
		
RMA_0395	RMA_0400	N	Y	N	RMA_0367	RMA_0429
	RMA_0395	2	11	0.491674	VirB9
	RMA_0396	0	13	1.156217	virulence protein
	RMA_0397	-1	13	2.491830	hypothetical protein
	RMA_0398	-2	12	1.428534	virulence protein
	RMA_0399	-3	12	0.984905	VirB9
	RMA_0400	-3	12	0.244820	VirB10
	288#RMA_0395	TYPE4SSCAGX#Type IV secretion system CagX conjugation protein si...	40	8e-06
		>TYPE4SSCAGX#Type IV secretion system CagX conjugation protein
		           signature.
		          Length = 522
		
		 Score = 39.8 bits (92), Expect = 8e-06
		 Identities = 30/102 (29%), Positives = 48/102 (47%), Gaps = 14/102 (13%)
		
		Query: 162 HPEKYNFNYYISG---SEEIAPIKIFDDGEFTYLQFRDKNAEISGIFAVDDSLRESLVNY 218
		           +P   N+NYY +    S+ I P +IFDDG FTY  F++   +   IF V    + S+ + 
		Sbjct: 395 NPVPRNYNYYQAPEKRSKHIMPSEIFDDGTFTYFGFKNITLQ-PAIFVVQPDGKLSMTD- 452
		
		Query: 219 RLAQDNPNMVIL-------EQVFPKLAIRKGKKVTCVFNQSF 253
		             A  +PNM           ++  K  + K K +  V N+ +
		Sbjct: 453 --AAIDPNMTNSGLRWYRVNEIAEKFKLIKDKALVTVINKGY 492
		
		
		
		 Score = 33.6 bits (76), Expect = 6e-04
		 Identities = 15/33 (45%), Positives = 20/33 (60%)
		
		Query: 61 IELARDEEIVSISMGDTTSWQIVPAGHRIFIKP 93
		          I+L +DE I  I+ G    W IVP  + IFI+P
		Sbjct: 67 IQLEKDETISYITTGFNKGWSIVPNSNHIFIQP 99
		
		
	289#RMA_0396	PF04335#VirB8 type IV secretion protein	193	3e-64
		>PF04335#VirB8 type IV secretion protein
		          Length = 227
		
		 Score =  193 bits (493), Expect = 3e-64
		 Identities = 42/211 (19%), Positives = 68/211 (32%), Gaps = 2/211 (0%)
		
		Query: 22  KSGEYFIDARKWYNFKYILPLSHRSLLLLICTIFTLLLTLICININILLPTNQKVSYLIK 81
		           +   YF +A  W   K       + L  ++  +   L T   + +  L P      Y+I 
		Sbjct: 9   ELKAYFEEAASWERDKLAAAERSKKLAWVVAGVAGALATAGVVAVAALTPLKTVEPYVIT 68
		
		Query: 82  DDAEKQAA-ITNTKHSTLANPYI-SVANIMLQNYVNQREEYNYDILKEQFTFIKNASTSI 139
		            D     A I    H      Y  +V    L  YV  RE +     +E F  +   S   
		Sbjct: 69  VDRNTGEASIAAKLHGDATITYDEAVRKYFLATYVRYREGWIAAAREEYFDAVMVMSARP 128
		
		Query: 140 VYMQFANFMHIDNPLSPVIRYQKLYRRSINILSINNINDNEAVVTFESLAKNSTGAILEN 199
		              +++ F   DNP SP           + I  ++ +  N A V F   +   + +   +
		Sbjct: 129 EQDRWSRFYKTDNPQSPQNILANRTDVFVEIKRVSFLGGNVAQVYFTKESVTGSNSTKTD 188
		
		Query: 200 MVWEARIGFIMDSISTSTSPDMPFNFTVTSY 230
		            V   +                P  + V SY
		Sbjct: 189 AVATIKYKVDGTPSKEVDRFKNPLGYQVESY 219
		
		
	291#RMA_0398	PF04335#VirB8 type IV secretion protein	179	1e-58
		>PF04335#VirB8 type IV secretion protein
		          Length = 227
		
		 Score =  179 bits (456), Expect = 1e-58
		 Identities = 39/209 (18%), Positives = 82/209 (39%), Gaps = 4/209 (1%)
		
		Query: 36  TQNWYEERSDKLLVQRNLLIILIILLTIFMVISTLVIAFVVKSKQFDPFVIQLNSNTGRA 95
		             +W  ++       + L  ++  +         + +A +   K  +P+VI ++ NTG A
		Sbjct: 17  AASWERDKLAAAERSKKLAWVVAGVAGALATAGVVAVAALTPLKTVEPYVITVDRNTGEA 76
		
		Query: 96  SVVEPISSP-VLTTDESLTRYFIKKYITARETYNPVDFATIARTTIRLFSTSSVYYNYLG 154
		           S+   +     +T DE++ +YF+  Y+  RE +            + + S       +  
		Sbjct: 77  SIAAKLHGDATITYDEAVRKYFLATYVRYREGWIAAAR-EEYFDAVMVMSARPEQDRWSR 135
		
		Query: 155 YIR-NKDFDPTLKYKEENTTFLVIKSWSKIAADKYIVRFSVNETSGNQL-VYNKIAVVSY 212
		           + + +    P          F+ IK  S +  +   V F+    +G+     + +A + Y
		Sbjct: 136 FYKTDNPQSPQNILANRTDVFVEIKRVSFLGGNVAQVYFTKESVTGSNSTKTDAVATIKY 195
		
		Query: 213 AYVPMQLTDSELDVNPVGFQVNGYRVDDD 241
		                   + +   NP+G+QV  YR D +
		Sbjct: 196 KVDGTPSKEVDRFKNPLGYQVESYRADVE 224
		
		
	292#RMA_0399	TYPE4SSCAGX#Type IV secretion system CagX conjugation protein si...	31	0.001
		>TYPE4SSCAGX#Type IV secretion system CagX conjugation protein
		           signature.
		          Length = 522
		
		 Score = 31.3 bits (70), Expect = 0.001
		 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
		
		Query: 71  IEFAKNEEIQNIILGDAYAWKITPLANRLFIKPLEKDIRTNM 112
		           I+  K+E I  I  G    W I P +N +FI+P  K +++N+
		Sbjct: 67  IQLEKDETISYITTGFNKGWSIVPNSNHIFIQP--KSVKSNL 106
		
		
		
		 Score = 27.4 bits (60), Expect = 0.029
		 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
		
		Query: 93  TPLANRLFIKPLEKDIRTNMTIITNKRIYEFDIASTELMMGNERDLVYVIKFYYPKKN 150
		           +P  N + + P +   RTN+ + TNK +Y+F +   +    N       +K  YP+++
		Sbjct: 262 SPEDNSIELSPSDSAWRTNLVVRTNKALYQFILRIAQ--KDNFASAYLTVKLEYPQRH 317
		
		
	293#RMA_0400	PF03544#Gram-negative bacterial tonB protein	33	0.002
		>PF03544#Gram-negative bacterial tonB protein
		          Length = 243
		
		 Score = 32.6 bits (74), Expect = 0.002
		 Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 1/82 (1%)
		
		Query: 67  QIPSNIVKPVMEVD-DNIPEIPKLPDPPKLETPTAPPPPPVVKVPPVLPPTTPVEENKDK 125
		             P  +V+P  E +    P         K +    P P PV KV        PVE     
		Sbjct: 68  PPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVEQPKRDVKPVESRPAS 127
		
		Query: 126 TFPLPPVSLPSTSGTLVESDAE 147
		            F     + P++S     +   
		Sbjct: 128 PFENTAPARPTSSTATAATSKP 149
		
		
RMA_0731	RMA_0740	N	Y	Y	RMA_0714	RMA_0760
	RMA_0731	8	12	-0.504703	conjugative transfer protein TraG
	RMA_0732	7	13	-1.167129	hypothetical protein
	RMA_0733	7	15	-0.394316	putative conjugative transfer protein TraD
	RMA_0734	6	15	-0.578689	transposase
	RMA_0735	6	16	-0.334744	conjugal transfer protein TraA
	RMA_0736	6	21	-0.684348	transposase
	RMA_0739	8	21	-0.858387	hypothetical protein
	RMA_0740	7	18	0.153532	transposase
	530#RMA_0731	FLAGELLIN#Flagellin signature.	31	0.025
		>FLAGELLIN#Flagellin signature.
		          Length = 507
		
		 Score = 30.8 bits (69), Expect = 0.025
		 Identities = 35/261 (13%), Positives = 74/261 (28%), Gaps = 18/261 (6%)
		
		Query: 466 VASSIGTNIADNNLSIDNYSIGNRTIAQQNLTPTLQLAGGIIDDGGMRVTSTDNGRQVLT 525
		               + T+ A+NN ++D +     T              G I  G    T    G     
		Sbjct: 232 ANGQLTTDDAENNTAVDLFKTTKSTAGTAEAKAI----AGAIKGGKEGDTFDYKGVTFTI 287
		
		Query: 526 QAVDSLVNNYRSSKLLQDSYQSQFMSSQSYLDSLNDRYSDLTTTGNSIATEIGKRLSYEE 585
		                   N    K+       +   + + + +        T   +           +  
		Sbjct: 288 DTKTGNDGN---GKVSTTINGEKVTLTVADITAGAANVDAATLQSSKNVYTSVVNGQFTF 344
		
		Query: 586 AKSIGITDSQYLALQQMNSDSTSATDHTGSSNRKGTSTSATGSIGVNTMFGSGMTTVGSS 645
		                   ++   L+  N+    +      +     +     ++   TMF     +  S+
		Sbjct: 345 DDKTKNESAKLSDLEANNAVKGESKITVNGAEYTANAAGDKVTLAGKTMFIDKTASGVST 404
		
		Query: 646 NTLDQDQGKSVNQQQSY---NEALSKIKSATKD-----GRLSNANSNVQSLSNNLNSNFS 697
		              +       +        + ALSK+ +          R  +A +N+ +   NLNS  S
		Sbjct: 405 LINEDAAAAKKSTANPLASIDSALSKVDAVRSSLGAIQNRFDSAITNLGNTVTNLNSARS 464
		
		Query: 698 EQQSV--GQEIAQ-TKQNMQQ 715
		             +      E++  +K  + Q
		Sbjct: 465 RIEDADYATEVSNMSKAQILQ 485
		
		
	531#RMA_0732	SYCDCHAPRONE#Gram-negative bacterial type III secretion SycD cha...	48	6e-09
		>SYCDCHAPRONE#Gram-negative bacterial type III secretion SycD
		           chaperone signature.
		          Length = 168
		
		 Score = 48.4 bits (115), Expect = 6e-09
		 Identities = 16/97 (16%), Positives = 38/97 (39%)
		
		Query: 127 DFAEAYNNKGVSYKKLGKYQEAIRLYNIAIKYKPSFAEAYNNKGDTLNSLGKYQEAIENF 186
		           D  E   +   +  + GKY++A +++          +  +   G    ++G+Y  AI ++
		Sbjct: 34  DTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSY 93
		
		Query: 187 DLALKYAPRYPEAYYNKGISLINLGQHQEAIKNYDIS 223
		                   + P   ++    L+  G+  EA     ++
		Sbjct: 94  SYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLA 130
		
		
		
		 Score = 43.8 bits (103), Expect = 2e-07
		 Identities = 25/131 (19%), Positives = 46/131 (35%), Gaps = 3/131 (2%)
		
		Query: 224 LKYKPDYANAYYNKATSLMQLGKYQEAIKNFDSVIKYQCDNEDAYNLKGCIFSILGKQQE 283
		            +   D     Y+ A +  Q GKY++A K F ++      +   +   G     +G+   
		Sbjct: 29  NEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDL 88
		
		Query: 284 AIKNYDLAIKYKPNFAAAYCNKGTSFRKLGKYQDAIKSYDLA---IKYKSDYAESYLEKG 340
		           AI +Y               +      + G+  +A     LA   I  K+++ E      
		Sbjct: 89  AIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKTEFKELSTRVS 148
		
		Query: 341 IVLVNLGKYKE 351
		            +L  +   KE
		Sbjct: 149 SMLEAIKLKKE 159
		
		
		
		 Score = 42.2 bits (99), Expect = 7e-07
		 Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 3/106 (2%)
		
		Query: 62  EEYFNIGRSLYKLGKYKKAIKNYDLAIKYKTDCAKCYNNKGRALNELANHQEAITNYDLA 121
		           E+ +++  + Y+ GKY+ A K +          ++ +   G     +  +  AI +Y   
		Sbjct: 37  EQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYG 96
		
		Query: 122 IKYDIDFAEAYNNKGVSYKKLGKYQEAIRLYNIA---IKYKPSFAE 164
		              DI       +      + G+  EA     +A   I  K  F E
		Sbjct: 97  AIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKTEFKE 142
		
		
		
		 Score = 41.1 bits (96), Expect = 2e-06
		 Identities = 18/95 (18%), Positives = 30/95 (31%)
		
		Query: 164 EAYNNKGDTLNSLGKYQEAIENFDLALKYAPRYPEAYYNKGISLINLGQHQEAIKNYDIS 223
		           E   +        GKY++A + F             +   G     +GQ+  AI +Y   
		Sbjct: 37  EQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYG 96
		
		Query: 224 LKYKPDYANAYYNKATSLMQLGKYQEAIKNFDSVI 258
		                      ++ A  L+Q G+  EA        
		Sbjct: 97  AIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQ 131
		
		
		
		 Score = 35.3 bits (81), Expect = 2e-04
		 Identities = 23/131 (17%), Positives = 43/131 (32%), Gaps = 10/131 (7%)
		
		Query: 178 KYQEAIENF-----DLA--LKYAPRYPEAYYNKGISLINLGQHQEAIKNYDISLKYKPDY 230
		           +YQ A+E+F      +A   + +    E  Y+   +    G++++A K +          
		Sbjct: 10  EYQLAMESFLKGGGTIAMLNEISSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYD 69
		
		Query: 231 ANAYYNKATSLMQLGKYQEAIKNFDSVIKYQCDNEDAYNLKGCIFSILGKQQEAIKNYDL 290
		           +  +         +G+Y  AI ++                        G+  EA     L
		Sbjct: 70  SRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFL 129
		
		Query: 291 A---IKYKPNF 298
		           A   I  K  F
		Sbjct: 130 AQELIADKTEF 140
		
		
		
		 Score = 34.5 bits (79), Expect = 3e-04
		 Identities = 15/87 (17%), Positives = 28/87 (32%)
		
		Query: 112 QEAITNYDLAIKYDIDFAEAYNNKGVSYKKLGKYQEAIRLYNIAIKYKPSFAEAYNNKGD 171
		           ++A   +      D   +  +   G   + +G+Y  AI  Y+              +  +
		Sbjct: 53  EDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAE 112
		
		Query: 172 TLNSLGKYQEAIENFDLALKYAPRYPE 198
		            L   G+  EA     LA +      E
		Sbjct: 113 CLLQKGELAEAESGLFLAQELIADKTE 139
		
		
		
		 Score = 33.7 bits (77), Expect = 6e-04
		 Identities = 20/97 (20%), Positives = 32/97 (32%), Gaps = 1/97 (1%)
		
		Query: 263 DNEDAYNLKGCIFSILGKQQEAIKNYDLAIKYKPNFAAAYCNKGTSFRKLGKYQDAIKSY 322
		             E  Y+L        GK ++A K +          +  +   G   + +G+Y  AI SY
		Sbjct: 35  TLEQLYSL-AFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSY 93
		
		Query: 323 DLAIKYKSDYAESYLEKGIVLVNLGKYKEAKENFNLA 359
		                               L+  G+  EA+    LA
		Sbjct: 94  SYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLA 130
		
		
		
		 Score = 28.7 bits (64), Expect = 0.024
		 Identities = 15/86 (17%), Positives = 28/86 (32%)
		
		Query: 304 NKGTSFRKLGKYQDAIKSYDLAIKYKSDYAESYLEKGIVLVNLGKYKEAKENFNLAFKYK 363
		           +   +  + GKY+DA K +          +  +L  G     +G+Y  A  +++      
		Sbjct: 41  SLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMD 100
		
		Query: 364 SNLIEEYEAIIKALRQLGNDLMANEF 389
		                      + L Q G    A   
		Sbjct: 101 IKEPRFPFHAAECLLQKGELAEAESG 126
		
		
	533#RMA_0734	FLGFLIH#Flagellar assembly protein FliH signature.	35	3e-04
		>FLGFLIH#Flagellar assembly protein FliH signature.
		          Length = 228
		
		 Score = 34.8 bits (79), Expect = 3e-04
		 Identities = 16/38 (42%), Positives = 25/38 (65%)
		
		Query: 277 EGLQVGKAQGIQIGEAKGIQIGEAKGIQIGKAEGKAEE 314
		           +G Q G A+G Q G  +G Q G A+G++ G AE K+++
		Sbjct: 54  QGYQAGIAEGRQQGHKQGYQEGLAQGLEQGLAEAKSQQ 91
		
		
		
		 Score = 32.8 bits (74), Expect = 0.001
		 Identities = 15/36 (41%), Positives = 22/36 (61%)
		
		Query: 267 QQEGKELGILEGLQVGKAQGIQIGEAKGIQIGEAKG 302
		            ++G + GI EG Q G  QG Q G A+G++ G A+ 
		Sbjct: 52  HEQGYQAGIAEGRQQGHKQGYQEGLAQGLEQGLAEA 87
		
		
	537#RMA_0740	HTHFIS#FIS bacterial regulatory protein HTH signature.	28	0.035
		>HTHFIS#FIS bacterial regulatory protein HTH signature.
		          Length = 484
		
		 Score = 28.3 bits (63), Expect = 0.035
		 Identities = 9/22 (40%), Positives = 12/22 (54%)
		
		Query: 103 NLLIFGPSGVGKSHLAAAIGYA 124
		            L+I G SG GK  +A A+   
		Sbjct: 162 TLMITGESGTGKELVARALHDY 183
		
		
