BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 036977
(693 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 50/193 (25%), Positives = 83/193 (43%), Gaps = 39/193 (20%)
Query: 160 FDSRMKVFQDVMEALKDDKLN----IIGVYGMGGVGKTTLVKQVAKKVMEDKLIDKVVMA 215
F +R K+ + + L KLN + +YGM G GK+ L A+ V + L++
Sbjct: 126 FVTRKKLVHAIQQKLW--KLNGEPGWVTIYGMAGCGKSVL---AAEAVRDHSLLEGCFSG 180
Query: 216 EV----TQNPDPQKIQDKLASDLGMKFDLNDSIHHR--------ASRLRE-RLKQEKRVL 262
V D + KL +L M+ D +S R RLR L++ R L
Sbjct: 181 GVHWVSIGKQDKSGLLMKL-QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSL 239
Query: 263 IILDNIWTKLELDAVGIPSGDVDEKDREDDQRRCTIILTSRSRDLLCIDMNSQKIFWIDA 322
+ILD++W L A D+Q C I+LT+R + + M + + +++
Sbjct: 240 LILDDVWDPWVLKAF-------------DNQ--CQILLTTRDKSVTDSVMGPKHVVPVES 284
Query: 323 -LSKEEALHLAKL 334
L +E+ L + L
Sbjct: 285 GLGREKGLEILSL 297
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 47/191 (24%), Positives = 82/191 (42%), Gaps = 35/191 (18%)
Query: 160 FDSRMKVFQDVMEALKDDKLN----IIGVYGMGGVGKTTLVKQVAK--KVMEDKLIDKVV 213
F +R K+ + + L KLN + +YGM G GK+ L + + ++E V
Sbjct: 133 FVTRKKLVHAIQQKLW--KLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVH 190
Query: 214 MAEVTQNPDPQKIQDKLASDLGMKFDLNDSIHHR--------ASRLRE-RLKQEKRVLII 264
+ + D + KL +L M+ D +S R RLR L++ R L+I
Sbjct: 191 WVSIGKQ-DKSGLLMKL-QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLI 248
Query: 265 LDNIWTKLELDAVGIPSGDVDEKDREDDQRRCTIILTSRSRDLLCIDMNSQKIFWIDA-L 323
LD++W L A D+Q C I+LT+ + + M + + +++ L
Sbjct: 249 LDDVWDPWVLKAF-------------DNQ--CQILLTTSDKSVTDSVMGPKHVVPVESGL 293
Query: 324 SKEEALHLAKL 334
+E+ L + L
Sbjct: 294 GREKGLEILSL 304
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 70/165 (42%), Gaps = 29/165 (17%)
Query: 182 IGVYGMGGVGKTTLVKQVAK--KVMEDKLIDKVVMAEVTQNPDPQKIQDKLASDLGMKFD 239
+ ++GM G GK+ L + + ++E V V + D + KL +L + D
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKL-QNLCTRLD 213
Query: 240 LNDSIHHR--------ASRLR-ERLKQEKRVLIILDNIWTKLELDAVGIPSGDVDEKDRE 290
++S R RLR L++ R L+ILD++W L A
Sbjct: 214 QDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF------------- 260
Query: 291 DDQRRCTIILTSRSRDLLCIDMNSQKIFWID-ALSKEEALHLAKL 334
+C I+LT+R + + M + + ++ +L KE+ L + L
Sbjct: 261 --DSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSL 303
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 32.7 bits (73), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 71/165 (43%), Gaps = 29/165 (17%)
Query: 182 IGVYGMGGVGKTTLVKQVAK--KVMEDKLIDKVVMAEVTQNPDPQKIQDKLASDLGMKFD 239
+ ++GM G GK+ L + + ++E V V + D + KL +L + D
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKL-QNLCTRLD 207
Query: 240 LNDSIHHR--------ASRLR-ERLKQEKRVLIILDNIWTKLELDAVGIPSGDVDEKDRE 290
++S R RLR L++ R L+ILD++W L A
Sbjct: 208 QDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF------------- 254
Query: 291 DDQRRCTIILTSRSRDLLCIDMNSQKIFWID-ALSKEEALHLAKL 334
D Q C I+LT+R + + M + + ++ +L KE+ L + L
Sbjct: 255 DSQ--CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSL 297
>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex
With Dna
Length = 387
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 51/103 (49%), Gaps = 8/103 (7%)
Query: 173 ALKDDKLNIIGVYGMGGVGKTTLVKQVAKKVMEDK-----LIDKVVMAEVTQNPDPQKIQ 227
AL+ +K + +YG+ G GKT + + V ++ +E + ++ K + P ++
Sbjct: 38 ALRGEKPSNALLYGLTGTGKTAVARLVLRR-LEARASSLGVLVKPIYVNARHRETPYRVA 96
Query: 228 DKLASDLGMKFDLND-SIHHRASRLRERLKQEKRV-LIILDNI 268
+A +G++ S+ RL +RL + + + +I+LD I
Sbjct: 97 SAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEI 139
>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
Bound To Origin Dna (From S. Solfataricus)
Length = 386
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 5/98 (5%)
Query: 175 KDDKLNIIGVYGMGGVGKTTLVKQVAKKVMEDKLIDKV--VMAEVTQNPDPQKIQDKLAS 232
+++K N I +YG+ G GKT +VK V K + K + K V Q P ++ L
Sbjct: 41 REEKPNNIFIYGLTGTGKTAVVKFVLSK-LHKKFLGKFKHVYINTRQIDTPYRVLADLLE 99
Query: 233 DLGMKFDLND-SIHHRASRLRERLKQE-KRVLIILDNI 268
L +K SI RL + ++ +V+I+LD I
Sbjct: 100 SLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEI 137
>pdb|1SKY|E Chain E, Crystal Structure Of The Nucleotide Free Alpha3beta3
Sub-Complex Of F1-Atpase From The Thermophilic Bacillus
Ps3
Length = 473
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 142 YRPTPKSTGLNDGKDNEAFDSRMKVFQDVMEALKDDKLNIIGVYGMGGVGKTTLVKQVAK 201
+RP PK L + E ++ +KV + +K K IG++G GVGKT L++++
Sbjct: 119 HRPAPKFEEL--ATEVEILETGIKVVDLLAPYIKGGK---IGLFGGAGVGKTVLIQELIH 173
Query: 202 KVMED 206
+ ++
Sbjct: 174 NIAQE 178
>pdb|2QE7|D Chain D, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
pdb|2QE7|E Chain E, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
pdb|2QE7|F Chain F, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
Length = 462
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 142 YRPTPKSTGLNDGKDNEAFDSRMKVFQDVMEALKDDKLNIIGVYGMGGVGKTTLVKQVAK 201
+RP P+ L+ +E ++ +KV + K K IG++G GVGKT L++++
Sbjct: 112 HRPAPEFEELSTA--DEILETGIKVIDLLAPYAKGGK---IGLFGGAGVGKTVLIQELIN 166
Query: 202 KVMED 206
V ++
Sbjct: 167 NVAQE 171
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 137 FSNVSYRPTPKSTGLNDGKDNEAFDSRMKVFQDVMEALKDDKLNIIGVYGMGGVGKTTLV 196
S + P P DG+ E +R ++V ++K + V G+ G GK+TLV
Sbjct: 610 LSGKKFIPIPAERRRPDGRWLEVVGAREHNLKNV--SVKIPLGTFVAVTGVSGSGKSTLV 667
Query: 197 KQVAKKVMEDKL 208
+V K + KL
Sbjct: 668 NEVLYKALAQKL 679
>pdb|2R6F|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Uvra
pdb|2R6F|B Chain B, Crystal Structure Of Bacillus Stearothermophilus Uvra
Length = 972
Score = 28.9 bits (63), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 137 FSNVSYRPTPKSTGLNDGKDNEAFDSRMKVFQDVMEALKDDKLNIIGVYGMGGVGKTTLV 196
S + P P DG+ E +R ++V ++K + V G+ G GK+TLV
Sbjct: 610 LSGKKFIPIPAERRRPDGRWLEVVGAREHNLKNV--SVKIPLGTFVAVTGVSGSGKSTLV 667
Query: 197 KQVAKKVMEDKL 208
+V K + KL
Sbjct: 668 NEVLYKALAQKL 679
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,974,686
Number of Sequences: 62578
Number of extensions: 836798
Number of successful extensions: 2368
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 2320
Number of HSP's gapped (non-prelim): 59
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)