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= 046770
(475 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 55/128 (42%), Gaps = 30/128 (23%)
Query: 304 RFLLVLDDVWNENYNDWIDLSRPFQDGAPGSKIIITTRNADAA-LIMGTVQAYPL----- 357
R LL+LDDVW+ W+ + +I++TTR+ +MG P+
Sbjct: 237 RSLLILDDVWDS----WV-----LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 358 --KGLSNDDCMCLFTQHSLETRDFSMHQPLKEIGAKIVIKCNGLPLAAKALGCLLHGKYD 415
KGL + + LF +++ D L E I+ +C G PL +G LL
Sbjct: 288 KEKGL---EILSLFV--NMKKAD------LPEQAHSIIKECKGSPLVVSLIGALLRDF-- 334
Query: 416 PSDWESVL 423
P+ WE L
Sbjct: 335 PNRWEYYL 342
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 33.1 bits (74), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 49/112 (43%), Gaps = 22/112 (19%)
Query: 304 RFLLVLDDVWNENYNDWIDLSRPFQDGAPGSKIIITTRNADAA-LIMGTVQAYPLK-GLS 361
R LL+LDDVW+ W+ + F + +I++TTR+ +MG P++ GL
Sbjct: 237 RSLLILDDVWDP----WV--LKAFDNQC---QILLTTRDKSVTDSVMGPKHVVPVESGLG 287
Query: 362 ND---DCMCLFTQHSLETRDFSMHQPLKEIGAKIVIKCNGLPLAAKALGCLL 410
+ + + LF E H +KE C G PL +G LL
Sbjct: 288 REKGLEILSLFVNMKKEDLPAEAHSIIKE--------CKGSPLVVSLIGALL 331
>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 = 32.3 bits (72), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 53/124 (42%), Gaps = 22/124 (17%)
Query: 304 RFLLVLDDVWNENYNDWIDLSRPFQDGAPGSKIIITTRNADAA-LIMGTVQAYPLKGLSN 362
R LL+LDDVW+ W+ + Q +I++TTR+ +MG P++
Sbjct: 243 RSLLILDDVWDS----WVLKAFDSQ-----CQILLTTRDKSVTDSVMGPKYVVPVES--- 290
Query: 363 DDCMCLFTQHSLETRDFSMHQP---LKEIGAKIVIKCNGLPLAAKALGCLLHGKYDPSDW 419
L + LE ++ L E I+ +C G PL +G LL + P+ W
Sbjct: 291 ----SLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRW 344
Query: 420 ESVL 423
E L
Sbjct: 345 EYYL 348
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
Length = 327
Score = 32.0 bits (71), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 27 IEMLLEKLASEAVVLFARRERIHDYLVQWKKTLEKIKAVIEDAEEK 72
I+ L EKL A V++ RR + Y V+ TLE ++ ++E AE++
Sbjct: 197 IDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQ 242
>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
Its Rna Complex: Rna-Protein Recognition Through A
Combination Of Rigid Docking And Induced Fit
Length = 314
Score = 32.0 bits (71), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 27 IEMLLEKLASEAVVLFARRERIHDYLVQWKKTLEKIKAVIEDAEEK 72
I+ L EKL A V++ RR + Y V+ TLE ++ ++E AE++
Sbjct: 184 IDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQ 229
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
Trub Bound To A T Stem-Loop Rna
Length = 327
Score = 32.0 bits (71), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 27 IEMLLEKLASEAVVLFARRERIHDYLVQWKKTLEKIKAVIEDAEEK 72
I+ L EKL A V++ RR + Y V+ TLE ++ ++E AE++
Sbjct: 197 IDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQ 242
>pdb|1M6D|A Chain A, Crystal Structure Of Human Cathepsin F
pdb|1M6D|B Chain B, Crystal Structure Of Human Cathepsin F
Length = 214
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 9/90 (10%)
Query: 58 TLEKIKAVIEDAEEKQTREESVKMWLYELQNLAYDVEDLLGEFETEALRRKL--LLEPAA 115
+ EK K I+D+ E E+ + WL + ++ + +F + R L L P
Sbjct: 99 SAEKAKVYIQDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWL 158
Query: 116 ADH-------HQPSTSKFPKFIRTWGTNLG 138
DH Q S F +WGT+ G
Sbjct: 159 IDHAVLLVGYGQRSDVPFWAIKNSWGTDWG 188
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 48/112 (42%), Gaps = 22/112 (19%)
Query: 304 RFLLVLDDVWNENYNDWIDLSRPFQDGAPGSKIIITTRNADAA-LIMGTVQAYPLK-GLS 361
R LL+LDDVW+ W+ + F + +I++TT + +MG P++ GL
Sbjct: 244 RSLLILDDVWDP----WV--LKAFDNQC---QILLTTSDKSVTDSVMGPKHVVPVESGLG 294
Query: 362 ND---DCMCLFTQHSLETRDFSMHQPLKEIGAKIVIKCNGLPLAAKALGCLL 410
+ + + LF E H +KE C G PL +G LL
Sbjct: 295 REKGLEILSLFVNMKKEDLPAEAHSIIKE--------CKGSPLVVSLIGALL 338
>pdb|3NAZ|A Chain A, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|B Chain B, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|C Chain C, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|D Chain D, Basal State Form Of Yeast Glycogen Synthase
pdb|3NCH|A Chain A, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|B Chain B, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|C Chain C, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|D Chain D, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3O3C|A Chain A, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|B Chain B, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|C Chain C, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|D Chain D, Glycogen Synthase Basal State Udp Complex
pdb|3RSZ|A Chain A, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|B Chain B, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|C Chain C, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|D Chain D, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
Length = 725
Score = 28.9 bits (63), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 11 RFRNQKETMSKIVSVSIEMLLEKLASEAVVLFARRERIHDYLVQWKKT-LEKIKA 64
RF+ E++ ++V +E ++K A++A+ R ER+ D L+ WK+ LE +KA
Sbjct: 577 RFKAPDESVEQLVDY-MEEFVKKTAAQAINQRNRTERLSD-LLDWKRMGLEYVKA 629
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
0.320 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,682,528
Number of Sequences: 62578
Number of extensions: 540312
Number of successful extensions: 1790
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1778
Number of HSP's gapped (non-prelim): 18
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)