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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, 8 months ago) by hstehr
File size: 11923 byte(s)
Log Message:
adding Model-It server files to repository
Line File contents
1 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)