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root/owl/trunk/modelit/server/results/MLH1_WT_1-340/MLH1_WT_1-340.pdb-blast.classic.out
Revision: 1299
Committed: Tue Jan 11 17:38:33 2011 UTC (8 years, 9 months ago) by hstehr
File size: 11923 byte(s)
Log Message:
adding Model-It server files to repository
Line User Rev File contents
1 hstehr 1299 BLASTP 2.2.18 [Mar-02-2008]
2    
3    
4     Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
5     Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
6     "Gapped BLAST and PSI-BLAST: a new generation of protein database search
7     programs", Nucleic Acids Res. 25:3389-3402.
8    
9     Reference for compositional score matrix adjustment: Altschul, Stephen F.,
10     John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
11     Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
12     using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
13    
14     Query= MLH1_HUMAN P40692 DNA mismatch repair protein Mlh1 OS=Homo
15     sapiens GN=MLH1 PE=1 SV=1
16     (340 letters)
17    
18     Database: seqs_pdbase_20080903.fix.reps.fa
19     20,430 sequences; 4,636,376 total letters
20    
21     Searching..................................................done
22    
23    
24    
25     Score E
26     Sequences producing significant alignments: (bits) Value
27    
28     pdb|1B63|A protein 209 4e-55
29     pdb|1H7S|A B protein 168 1e-42
30     pdb|1VA6|A B protein 32 0.13
31     pdb|2P1G|A B protein 32 0.23
32     pdb|1A6T|B D protein 29 1.2
33     pdb|1GZ7|A B C D protein 29 1.3
34     pdb|1GDJ|A protein 29 1.4
35     pdb|1GKZ|A protein 28 2.1
36     pdb|1YSR|A B C protein 28 2.3
37     pdb|1Q0P|A protein 28 2.4
38     pdb|2C2A|A protein 28 2.6
39     pdb|2OK5|A protein 28 3.3
40     pdb|1RRK|A protein 27 3.9
41     pdb|2OCD|A B C D protein 27 4.9
42     pdb|2FOK|A B protein 26 8.1
43     pdb|2D7P|A protein 26 9.7
44    
45     >pdb|1B63|A protein
46     Length = 333
47    
48     Score = 209 bits (533), Expect = 4e-55, Method: Compositional matrix adjust.
49     Identities = 119/331 (35%), Positives = 191/331 (57%), Gaps = 7/331 (2%)
50    
51     Query: 8 IRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTG 67
52     I+ L + N+IAAGEV++RPA+ +KE++EN LDA +T I + ++ GG KLI+I+DNG G
53     Sbjct: 5 IQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCG 64
54    
55     Query: 68 IRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYR 127
56     I+K++L + R TSK+ S +DL +I + GFRGEALASIS V+ +T+T++TA+ + A++
57     Sbjct: 65 IKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQ 124
58    
59     Query: 128 ASYSDGK-LKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVH 186
60     A Y++G+ + KP A GT + V DLFYN RRK L+ E+ I E++ R ++
61     Sbjct: 125 A-YAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALA 183
62    
63     Query: 187 NAGISFSVKKQGETVADVRTLPNASTVD-NIRSIFGNAVSRELIEIGCEDKTLAFKMNGY 245
64     ++ ++ G+ V R +P + + +I G A + + I + L + G+
65     Sbjct: 184 RFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLR--GW 241
66    
67     Query: 246 ISNANYSVKKC--IFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNV 303
68     +++ N++ I ++N R++ + AI L + P L LEI P V
69     Sbjct: 242 VADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQV 301
70    
71     Query: 304 DVNVHPTKHEVHFLHEESILERVQQHIESKL 334
72     DVNVHP KHEV F + + + Q + S L
73     Sbjct: 302 DVNVHPAKHEVRFHQSRLVHDFIYQGVLSVL 332
74    
75    
76     >pdb|1H7S|A B protein
77     Length = 365
78    
79     Score = 168 bits (425), Expect = 1e-42, Method: Compositional matrix adjust.
80     Identities = 115/359 (32%), Positives = 196/359 (54%), Gaps = 36/359 (10%)
81    
82     Query: 5 AGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDN 64
83     A I+ +D V++I +G+V+ + A+KE++EN LDA +T+I + +K+ G+ LI++ DN
84     Sbjct: 12 AKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDN 71
85    
86     Query: 65 GTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKC 124
87     G G+ +E+ + + + TSK+Q F DL + T+GFRGEAL+S+ ++ VTI+T A K
88     Sbjct: 72 GCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKV 131
89    
90     Query: 125 AYRASYS-DGKL--KAP-PKPCAGNQGTQITVEDLFYNIATRRKAL-KNPSEEYGKILEV 179
91     R + +GK+ K P P+P +GT ++V+ LF + R K +N +EY K ++V
92     Sbjct: 132 GTRLXFDHNGKIIQKTPYPRP----RGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKXVQV 187
93    
94     Query: 180 VGRYSVHNAGISFSVKK---QGETVADVRTLPNASTVDNIRSIFGNAVSRELIEI----- 231
95     + Y + +AGI S QG+ V T + S +NI S+FG + LI
96     Sbjct: 188 LHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPP 247
97    
98     Query: 232 ---GCEDKTLA--------FKMNGYISNANYSVKKCIF---LLFINHRLVESTSLRKAIE 277
99     CE+ L+ F ++G+IS + V + FIN R + + + +
100     Sbjct: 248 SDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVN 307
101    
102     Query: 278 TVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLLG 336
103     VY Y ++ +PF+ L++ + + VD+NV P K ++ L EE +L V +++ L+G
104     Sbjct: 308 EVYHXY-NRHQYPFVVLNISVDSECVDINVTPDKRQI-LLQEEKLLLAV---LKTSLIG 361
105    
106    
107     >pdb|1VA6|A B protein
108     Length = 518
109    
110     Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
111     Identities = 14/27 (51%), Positives = 19/27 (70%)
112    
113     Query: 150 ITVEDLFYNIATRRKALKNPSEEYGKI 176
114     IT DL+ +A ++A+K PSEEY KI
115     Sbjct: 251 ITFNDLYEYVAGLKQAIKTPSEEYAKI 277
116    
117    
118     >pdb|2P1G|A B protein
119     Length = 249
120    
121     Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
122     Identities = 29/95 (30%), Positives = 44/95 (46%), Gaps = 24/95 (25%)
123    
124     Query: 241 KMNGYISNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLP---------KNTHPF 291
125     K++GY S +Y +IN+ + + +E V AAY P +THP
126     Sbjct: 81 KIDGYTSRLHYISD------WINNAVRQGL-----LEDVTAAYSPFKQKLSLSYMSTHPE 129
127    
128     Query: 292 LYLSLEISPQNVDVNVHPTK----HEVHFLHEESI 322
129     LY SL+ SP+NV K EVH+L ++ +
130     Sbjct: 130 LYKSLKNSPENVAQMAKYEKALSGKEVHYLPKDKL 164
131    
132    
133     >pdb|1A6T|B D protein
134     Length = 217
135    
136     Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
137     Identities = 13/34 (38%), Positives = 20/34 (58%)
138    
139     Query: 171 EEYGKILEVVGRYSVHNAGISFSVKKQGETVADV 204
140     + +GK LE +GR N G SF+ K +G+ + V
141     Sbjct: 39 QSHGKSLEWIGRVDPDNGGTSFNQKFKGKAILTV 72
142    
143    
144     >pdb|1GZ7|A B C D protein
145     Length = 534
146    
147     Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
148     Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 6/104 (5%)
149    
150     Query: 50 IVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFE-DLASISTYGFRGEALASIS 108
151     + G L IQ+ G+G + ++ + F D + ++ YG E+ S+S
152     Sbjct: 158 VASWGFLAGPDIQNEGSGNAGLHDQRLAMQWVADNIAGFGGDPSKVTIYG---ESAGSMS 214
153    
154     Query: 109 HVAHVTITT--KTADGKCAYRASYSDGKLKAPPKPCAGNQGTQI 150
155     H+ T +GK +RA+ P P G GT+I
156     Sbjct: 215 TFVHLVWNDGDNTYNGKPLFRAAIMQSGCMVPSDPVDGTYGTEI 258
157    
158    
159     >pdb|1GDJ|A protein
160     Length = 153
161    
162     Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
163     Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
164    
165     Query: 266 LVES-TSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDV 305
166     L ES +L K+ + A +PK+TH F L LEI+P D+
167     Sbjct: 3 LTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDL 43
168    
169    
170     >pdb|1GKZ|A protein
171     Length = 388
172    
173     Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
174     Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
175    
176     Query: 30 NAIKEMIENCLDAKSTSIQVIVKEGGLK---LIQIQDNGTGIRKEDLDIVCE-RFTTSK 84
177     NA++ +E+ LD V++ +I+I D G GI +DLD V + FTT++
178     Sbjct: 249 NAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAE 307
179    
180    
181     >pdb|1YSR|A B C protein
182     Length = 150
183    
184     Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
185     Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 13/53 (24%)
186    
187     Query: 42 AKSTSIQVIVKEGGLKLIQ-------------IQDNGTGIRKEDLDIVCERFT 81
188     A +I VK GG L+Q I DNG+G+ + + +V ERF+
189     Sbjct: 50 AVDNAIANAVKHGGATLVQLSAVSSRAGVEIAIDDNGSGVPEGERQVVFERFS 102
190    
191    
192     >pdb|1Q0P|A protein
193     Length = 223
194    
195     Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
196     Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
197    
198     Query: 247 SNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAY-LPKNTHP 290
199     SNA++ K+ + + +H+L T+ +KA++ VY+ P + P
200     Sbjct: 77 SNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPP 121
201    
202    
203     >pdb|2C2A|A protein
204     Length = 258
205    
206     Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
207     Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
208    
209     Query: 41 DAKSTSIQVIV--KEGGLKLIQIQDNGTGIRKEDLDIVCERF 80
210     DA ++VI+ K+GG+ LI ++DNG GI D + E+F
211     Sbjct: 157 DAPDKYVKVILDEKDGGV-LIIVEDNGIGIPDHAKDRIFEQF 197
212    
213    
214     >pdb|2OK5|A protein
215     Length = 752
216    
217     Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
218     Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
219    
220     Query: 247 SNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAY-LPKNTHP 290
221     SNA++ K+ + + +H+L T+ +KA++ VY+ P + P
222     Sbjct: 315 SNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPP 359
223    
224    
225     >pdb|1RRK|A protein
226     Length = 497
227    
228     Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
229     Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
230    
231     Query: 247 SNANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAY-LPKNTHP 290
232     SNA++ K+ + + +H+L T+ +KA++ VY+ P + P
233     Sbjct: 63 SNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPP 107
234    
235    
236     >pdb|2OCD|A B C D protein
237     Length = 337
238    
239     Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
240     Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
241    
242     Query: 249 ANYSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLY--LSLEISPQNVDVN 306
243     ANY + + LF N+RL RK+ ++A+ N P L +++E+S NV V+
244     Sbjct: 140 ANYPINEVT--LFFNNRLXRGNRSRKSHADGFSAFSSPNLPPLLEAGINIELS-TNVKVD 196
245    
246     Query: 307 VHPT 310
247     P+
248     Sbjct: 197 EKPS 200
249    
250    
251     >pdb|2FOK|A B protein
252     Length = 579
253    
254     Score = 26.2 bits (56), Expect = 8.1, Method: Compositional matrix adjust.
255     Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
256    
257     Query: 47 IQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCE 78
258     +++++K G LK+ QIQDN ++K D V E
259     Sbjct: 314 LEILIKAGSLKIEQIQDN---LKKLGFDEVIE 342
260    
261    
262     >pdb|2D7P|A protein
263     Length = 112
264    
265     Score = 26.2 bits (56), Expect = 9.7, Method: Compositional matrix adjust.
266     Identities = 13/44 (29%), Positives = 24/44 (54%)
267    
268     Query: 25 IQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGI 68
269     + P+ A++E + LD+ +I+ I E G+ I ++ NG I
270     Sbjct: 47 VHTPSGAVEECYVSELDSDKHTIRFIPHENGVHSIDVKFNGAHI 90
271    
272    
273     Database: seqs_pdbase_20080903.fix.reps.fa
274     Posted date: Sep 3, 2008 11:00 PM
275     Number of letters in database: 4,636,376
276     Number of sequences in database: 20,430
277    
278     Lambda K H
279     0.317 0.132 0.369
280    
281     Gapped
282     Lambda K H
283     0.267 0.0410 0.140
284    
285    
286     Matrix: BLOSUM62
287     Gap Penalties: Existence: 11, Extension: 1
288     Number of Sequences: 20430
289     Number of Hits to DB: 2,885,479
290     Number of extensions: 112747
291     Number of successful extensions: 306
292     Number of sequences better than 10.0: 18
293     Number of HSP's gapped: 303
294     Number of HSP's successfully gapped: 18
295     Length of query: 340
296     Length of database: 4,636,376
297     Length adjustment: 92
298     Effective length of query: 248
299     Effective length of database: 2,756,816
300     Effective search space: 683690368
301     Effective search space used: 683690368
302     Neighboring words threshold: 11
303     Window for multiple hits: 40
304     X1: 16 ( 7.3 bits)
305     X2: 38 (14.6 bits)
306     X3: 64 (24.7 bits)
307     S1: 41 (21.7 bits)
308     S2: 56 (26.2 bits)