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= 042728
(486 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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 66/278 (23%), Positives = 114/278 (41%), Gaps = 51/278 (18%)
Query: 160 FDSRMKVFQDVMEALRDDKLN----IIGVHGMGGVGKTTIVKQVAK-QVMEENLFDKVVM 214
F +R K+ + + L KLN + ++GM G GK+ + + + + E F V
Sbjct: 126 FVTRKKLVHAIQQKLW--KLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVH 183
Query: 215 AEVTQTPDHHKIQNKLAFDLGMEFGLNENEFQR----AERLHERLK-----KEKQLLIIL 265
D + KL +L M E+ QR E +RL+ K + L+IL
Sbjct: 184 WVSIGKQDKSGLLMKLQ-NLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLIL 242
Query: 266 DNIWTKLELDKFGIPTGDVAEKDRKDDQRRCTIILTSRKQDLLRIDMNSQKNFQIDA-LP 324
D++W L F D+Q C I+LT+R + + M + +++ L
Sbjct: 243 DDVWDPWVLKAF-------------DNQ--CQILLTTRDKSVTDSVMGPKHVVPVESGLG 287
Query: 325 PKEALQLFEEIVGDSTKISAFQSTANEIVERCGGLPVALSTVANALKTKELDF---WKDA 381
++ L++ V + K + A+ I++ C G P+ +S + L+ DF W
Sbjct: 288 REKGLEILSLFV--NMKKEDLPAEAHSIIKECKGSPLVVSLIGALLR----DFPNRWAYY 341
Query: 382 LNQLRRSDAREIHGMQANVYTSIKLSYDFLESEEAKSL 419
L QL+ + I SYD+ +EA S+
Sbjct: 342 LRQLQNKQFKRIRKSS---------SYDYEALDEAMSI 370
>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 = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 58/252 (23%), Positives = 101/252 (40%), Gaps = 45/252 (17%)
Query: 182 IGVHGMGGVGKTTIVKQVAK-QVMEENLFDKVVMAEVTQTPDHHKIQNKLAFDLGMEFGL 240
+ +HGM G GK+ + + + + E F V D + KL +L
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQ-NLCTRLDQ 214
Query: 241 NENEFQR----AERLHERLK-----KEKQLLIILDNIWTKLELDKFGIPTGDVAEKDRKD 291
+E+ QR E +RL+ K + L+ILD++W L F
Sbjct: 215 DESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------------- 260
Query: 292 DQRRCTIILTSRKQDLLRIDMNSQKNFQIDALPPKE-ALQLFEEIVGDSTKISAFQSTAN 350
+C I+LT+R + + M + +++ KE L++ V + K + A+
Sbjct: 261 -DSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFV--NMKKADLPEQAH 317
Query: 351 EIVERCGGLPVALSTVANALKTKELDF---WKDALNQLRRSDAREIHGMQANVYTSIKLS 407
I++ C G P+ +S + L+ DF W+ L QL+ + I S
Sbjct: 318 SIIKECKGSPLVVSLIGALLR----DFPNRWEYYLKQLQNKQFKRIRKSS---------S 364
Query: 408 YDFLESEEAKSL 419
YD+ +EA S+
Sbjct: 365 YDYEALDEAMSI 376
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 59/252 (23%), Positives = 103/252 (40%), Gaps = 45/252 (17%)
Query: 182 IGVHGMGGVGKTTIVKQVAK-QVMEENLFDKVVMAEVTQTPDHHKIQNKLAFDLGMEFGL 240
+ +HGM G GK+ + + + + E F V D + KL +L
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQ-NLCTRLDQ 208
Query: 241 NENEFQR----AERLHERLK-----KEKQLLIILDNIWTKLELDKFGIPTGDVAEKDRKD 291
+E+ QR E +RL+ K + L+ILD++W L F D
Sbjct: 209 DESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF-------------D 255
Query: 292 DQRRCTIILTSRKQDLLRIDMNSQKNFQID-ALPPKEALQLFEEIVGDSTKISAFQSTAN 350
Q C I+LT+R + + M + ++ +L ++ L++ V + K + A+
Sbjct: 256 SQ--CQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFV--NMKKADLPEQAH 311
Query: 351 EIVERCGGLPVALSTVANALKTKELDF---WKDALNQLRRSDAREIHGMQANVYTSIKLS 407
I++ C G P+ +S + L+ DF W+ L QL+ + I S
Sbjct: 312 SIIKECKGSPLVVSLIGALLR----DFPNRWEYYLKQLQNKQFKRIRKSS---------S 358
Query: 408 YDFLESEEAKSL 419
YD+ +EA S+
Sbjct: 359 YDYEALDEAMSI 370
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 65/278 (23%), Positives = 113/278 (40%), Gaps = 51/278 (18%)
Query: 160 FDSRMKVFQDVMEALRDDKLN----IIGVHGMGGVGKTTIVKQVAK-QVMEENLFDKVVM 214
F +R K+ + + L KLN + ++GM G GK+ + + + + E F V
Sbjct: 133 FVTRKKLVHAIQQKLW--KLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVH 190
Query: 215 AEVTQTPDHHKIQNKLAFDLGMEFGLNENEFQR----AERLHERLK-----KEKQLLIIL 265
D + KL +L M E+ QR E +RL+ K + L+IL
Sbjct: 191 WVSIGKQDKSGLLMKLQ-NLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLIL 249
Query: 266 DNIWTKLELDKFGIPTGDVAEKDRKDDQRRCTIILTSRKQDLLRIDMNSQKNFQIDA-LP 324
D++W L F D+Q C I+LT+ + + M + +++ L
Sbjct: 250 DDVWDPWVLKAF-------------DNQ--CQILLTTSDKSVTDSVMGPKHVVPVESGLG 294
Query: 325 PKEALQLFEEIVGDSTKISAFQSTANEIVERCGGLPVALSTVANALKTKELDF---WKDA 381
++ L++ V + K + A+ I++ C G P+ +S + L+ DF W
Sbjct: 295 REKGLEILSLFV--NMKKEDLPAEAHSIIKECKGSPLVVSLIGALLR----DFPNRWAYY 348
Query: 382 LNQLRRSDAREIHGMQANVYTSIKLSYDFLESEEAKSL 419
L QL+ + I SYD+ +EA S+
Sbjct: 349 LRQLQNKQFKRIRKSS---------SYDYEALDEAMSI 377
>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 = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 142 HRPTPKLAEHIQVKDFEAFDSRMKVFQDVMEALRDDKLNIIGVHGMGGVGKTTIVKQVAK 201
HRP PK E + E ++ +KV + ++ K IG+ G GVGKT +++++
Sbjct: 119 HRPAPKFEE--LATEVEILETGIKVVDLLAPYIKGGK---IGLFGGAGVGKTVLIQELIH 173
Query: 202 QVMEEN 207
+ +E+
Sbjct: 174 NIAQEH 179
>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 = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 142 HRPTPKLAEHIQVKDFEAFDSRMKVFQDVMEALRDDKLNIIGVHGMGGVGKTTIVKQVAK 201
HRP P+ E + D E ++ +KV + + K IG+ G GVGKT +++++
Sbjct: 112 HRPAPEF-EELSTAD-EILETGIKVIDLLAPYAKGGK---IGLFGGAGVGKTVLIQELIN 166
Query: 202 QVMEEN 207
V +E+
Sbjct: 167 NVAQEH 172
>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
Bound To Origin Dna (From S. Solfataricus)
Length = 386
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 53/99 (53%), Gaps = 7/99 (7%)
Query: 175 RDDKLNIIGVHGMGGVGKTTIVKQVAKQVMEENLFD-KVVMAEVTQTPDHHKIQNKL--A 231
R++K N I ++G+ G GKT +VK V ++ ++ L K V Q +++ L +
Sbjct: 41 REEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLES 100
Query: 232 FDLGMEF-GLNENEFQRAERLHERLKKE-KQLLIILDNI 268
D+ + F GL+ E R RL + ++ Q++I+LD I
Sbjct: 101 LDVKVPFTGLSIAELYR--RLVKAVRDYGSQVVIVLDEI 137
>pdb|1X9F|B Chain B, Hemoglobin Dodecamer From Lumbricus Erythrocruorin
pdb|1X9F|F Chain F, Hemoglobin Dodecamer From Lumbricus Erythrocruorin
pdb|1X9F|J Chain J, Hemoglobin Dodecamer From Lumbricus Erythrocruorin
pdb|2GTL|B Chain B, Lumbricus Erythrocruorin At 3.5a Resolution
pdb|2GTL|F Chain F, Lumbricus Erythrocruorin At 3.5a Resolution
pdb|2GTL|J Chain J, Lumbricus Erythrocruorin At 3.5a Resolution
Length = 145
Score = 29.6 bits (65), Expect = 4.3, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 327 EALQLFEEIVGDSTKISAFQSTANEIVERCGGLPVALSTVANALKTKE 374
E+ LF+ + GD T AF + A+ ++ GGL +A+ST+ KE
Sbjct: 43 ESRSLFKRVHGDDTSHPAFIAHADRVL---GGLDIAISTLDQPATLKE 87
>pdb|3OZX|A Chain A, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
pdb|3OZX|B Chain B, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
Length = 538
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 19/24 (79%)
Query: 181 IIGVHGMGGVGKTTIVKQVAKQVM 204
I+GV G GVGKTT++K +A +++
Sbjct: 27 ILGVLGKNGVGKTTVLKILAGEII 50
>pdb|1YQT|A Chain A, Rnase-L Inhibitor
Length = 538
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 7/47 (14%)
Query: 154 VKDFEAFDSRMKVFQDVMEALRDDKLNIIGVHGMGGVGKTTIVKQVA 200
VKD+ +F R++V E K +IG+ G G+GKTT VK +A
Sbjct: 294 VKDYGSF--RLEV-----EPGEIKKGEVIGIVGPNGIGKTTFVKXLA 333
>pdb|1VMA|A Chain A, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
pdb|1VMA|B Chain B, Crystal Structure Of Cell Division Protein Ftsy (Tm0570)
From Thermotoga Maritima At 1.60 A Resolution
Length = 306
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 138 SNVSHRPTPKLAEHIQVKDFEAFDSRMKVFQDVMEALRDDKLNI-------IGVHGMGGV 190
++V T + E ++ KD +A +S ++ +++ D KLN+ I V G+ G
Sbjct: 58 ADVGVETTEYILERLEEKDGDALESLKEIILEILNF--DTKLNVPPEPPFVIMVVGVNGT 115
Query: 191 GKTTIVKQVAKQVMEEN 207
GKTT ++AK ++E
Sbjct: 116 GKTTSCGKLAKMFVDEG 132
>pdb|1SGW|A Chain A, Putative Abc Transporter (Atp-Binding Protein) From
Pyrococcus Furiosus Pfu-867808-001
Length = 214
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 28/44 (63%), Gaps = 3/44 (6%)
Query: 177 DKLNIIGVHGMGGVGKTTIVKQVA---KQVMEENLFDKVVMAEV 217
+K N++ HG G+GKTT++K ++ K + E +++ V + +V
Sbjct: 33 EKGNVVNFHGPNGIGKTTLLKTISTYLKPLKGEIIYNGVPITKV 76
>pdb|2PZJ|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+
pdb|2Q1S|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nadh
pdb|2Q1T|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
pdb|2Q1U|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
pdb|2Q1U|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmf In Complex With Nad+ And Udp
Length = 377
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 162 SRMKVFQDVMEALRDDKLNIIGVHGMGGVGKTTIVKQVAKQVMEENLFDKVVMAEVTQTP 221
S M V +M A + N++ V G G VG + + + V + ++ D ++ AE P
Sbjct: 19 SHMPV---IMNASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVP 75
Query: 222 DHHKIQ 227
DH ++
Sbjct: 76 DHPAVR 81
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
0.318 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,222,238
Number of Sequences: 62578
Number of extensions: 523324
Number of successful extensions: 1637
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 1623
Number of HSP's gapped (non-prelim): 30
length of query: 486
length of database: 14,973,337
effective HSP length: 103
effective length of query: 383
effective length of database: 8,527,803
effective search space: 3266148549
effective search space used: 3266148549
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: 53 (25.0 bits)