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= 006107
(661 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 75/315 (23%), Positives = 125/315 (39%), Gaps = 54/315 (17%)
Query: 215 KTTLAREVYNDKAVADSKFDVKA-WVCVSDNFDVFNILKALLESITSAASDLNTLNEVQV 273
K+ LA E D ++ + F WV V D +L L T D + + +
Sbjct: 160 KSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPL 218
Query: 274 QLKKAVDGKRFL---------LVLDDVRNEDYSLWVDLKAPFLAAAPNSKMIITTRHSDV 324
+++A D R L L+LDDV + WV A ++++TTR V
Sbjct: 219 NIEEAKDRLRILMLRKHPRSLLILDDV----WDSWV-----LKAFDSQCQILLTTRDKSV 269
Query: 325 A-STMGPIEHYNLKSLLDDD----CWSIFIKHALEGRDLSAHQISESFRKKVVGKCRGLP 379
S MGP ++S L + S+F+ AH I + +C+G P
Sbjct: 270 TDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSI--------IKECKGSP 321
Query: 380 LAAKTLEGLLR--TTRHAAWDDILDSKIWDLHQQSS------ILPVLRLSYHHLPSHLKR 431
L + LLR R + L +K + ++SS + + +S L +K
Sbjct: 322 LVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKD 381
Query: 432 CFAFCAIFPKDYEFTEKGLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSS 491
+ +I KD + K L LW +E++ED+ + V++S+ +
Sbjct: 382 YYTDLSILQKDVKVPTKVLCILW--------DMETEEVEDI----LQEFVNKSLLFCDRN 429
Query: 492 GSS-KFVMHDLIHDF 505
G S ++ +HDL DF
Sbjct: 430 GKSFRYYLHDLQVDF 444
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 63/238 (26%), Positives = 101/238 (42%), Gaps = 45/238 (18%)
Query: 283 RFLLVLDDVRNEDYSLWVDLKAPFLAAAPN-SKMIITTRHSDVA-STMGPIEHYNLKSLL 340
R LL+LDDV + WV L A N ++++TTR V S MGP ++S L
Sbjct: 237 RSLLILDDV----WDPWV------LKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGL 286
Query: 341 DDD----CWSIFIKHALEGRDLSAHQISESFRKKVVGKCRGLPLAAKTLEGLLR--TTRH 394
+ S+F+ E AH I + +C+G PL + LLR R
Sbjct: 287 GREKGLEILSLFVNMKKEDLPAEAHSI--------IKECKGSPLVVSLIGALLRDFPNRW 338
Query: 395 AAWDDILDSKIWDLHQQSS------ILPVLRLSYHHLPSHLKRCFAFCAIFPKDYEFTEK 448
A + L +K + ++SS + + +S L +K + +I KD + K
Sbjct: 339 AYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTK 398
Query: 449 GLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSSGSS-KFVMHDLIHDF 505
L LW +E++ED+ + V++S+ +G S + +HDL DF
Sbjct: 399 VLCVLW--------DLETEEVEDI----LQEFVNKSLLFCNRNGKSFCYYLHDLQVDF 444
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 75/315 (23%), Positives = 125/315 (39%), Gaps = 54/315 (17%)
Query: 215 KTTLAREVYNDKAVADSKFDVKA-WVCVSDNFDVFNILKALLESITSAASDLNTLNEVQV 273
K+ LA E D ++ + F WV V D +L L T D + + +
Sbjct: 166 KSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPL 224
Query: 274 QLKKAVDGKRFL---------LVLDDVRNEDYSLWVDLKAPFLAAAPNSKMIITTRHSDV 324
+++A D R L L+LDDV + WV A ++++TTR V
Sbjct: 225 NIEEAKDRLRILMLRKHPRSLLILDDV----WDSWV-----LKAFDSQCQILLTTRDKSV 275
Query: 325 A-STMGPIEHYNLKSLLDDD----CWSIFIKHALEGRDLSAHQISESFRKKVVGKCRGLP 379
S MGP ++S L + S+F+ AH I + +C+G P
Sbjct: 276 TDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSI--------IKECKGSP 327
Query: 380 LAAKTLEGLLR--TTRHAAWDDILDSKIWDLHQQSS------ILPVLRLSYHHLPSHLKR 431
L + LLR R + L +K + ++SS + + +S L +K
Sbjct: 328 LVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKD 387
Query: 432 CFAFCAIFPKDYEFTEKGLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSS 491
+ +I KD + K L LW +E++ED+ + V++S+ +
Sbjct: 388 YYTDLSILQKDVKVPTKVLCILW--------DMETEEVEDI----LQEFVNKSLLFCDRN 435
Query: 492 GSS-KFVMHDLIHDF 505
G S ++ +HDL DF
Sbjct: 436 GKSFRYYLHDLQVDF 450
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 62/238 (26%), Positives = 100/238 (42%), Gaps = 45/238 (18%)
Query: 283 RFLLVLDDVRNEDYSLWVDLKAPFLAAAPN-SKMIITTRHSDVA-STMGPIEHYNLKSLL 340
R LL+LDDV + WV L A N ++++TT V S MGP ++S L
Sbjct: 244 RSLLILDDV----WDPWV------LKAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGL 293
Query: 341 DDD----CWSIFIKHALEGRDLSAHQISESFRKKVVGKCRGLPLAAKTLEGLLR--TTRH 394
+ S+F+ E AH I + +C+G PL + LLR R
Sbjct: 294 GREKGLEILSLFVNMKKEDLPAEAHSI--------IKECKGSPLVVSLIGALLRDFPNRW 345
Query: 395 AAWDDILDSKIWDLHQQSS------ILPVLRLSYHHLPSHLKRCFAFCAIFPKDYEFTEK 448
A + L +K + ++SS + + +S L +K + +I KD + K
Sbjct: 346 AYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTK 405
Query: 449 GLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSSGSS-KFVMHDLIHDF 505
L LW +E++ED+ + V++S+ +G S + +HDL DF
Sbjct: 406 VLCVLW--------DLETEEVEDI----LQEFVNKSLLFCNRNGKSFCYYLHDLQVDF 451
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 64 DEAVKMWLDELQDLAYDAEDILDEFATQA 92
D K+W DE+++L+Y ED++D+F Q
Sbjct: 54 DSQDKLWADEVRELSYVIEDVVDKFLVQV 82
>pdb|3TIG|A Chain A, Tubulin Tyrosine Ligase
pdb|3TII|A Chain A, Tubulin Tyrosine Ligase
pdb|3TII|B Chain B, Tubulin Tyrosine Ligase
pdb|3TIN|A Chain A, Tubulin Tyrosine Ligase
Length = 380
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 232 KFDVKAWVCVSDNFDVFNILKALLESITSAASDLN 266
KFD+++WV V + ++++ + +L + + SD N
Sbjct: 201 KFDIRSWVLVDNQYNIYLYREGVLRTSSEPYSDTN 235
>pdb|3F6O|A Chain A, Crystal Structure Of Arsr Family Transcriptional
Regulator, Rha00566
pdb|3F6O|B Chain B, Crystal Structure Of Arsr Family Transcriptional
Regulator, Rha00566
Length = 118
Score = 29.3 bits (64), Expect = 7.0, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 25 LLSFVRQLQVRVDSELKKWEKKLKMIQAVLCDAEEKQLTDEAVKMWLDELQDLAYDAEDI 84
L SF++ + DS W + K + C E++ T AV+ WL E Q+L D
Sbjct: 45 LPSFMKHIHFLEDS---GWIRTHKQGRVRTCAIEKEPFT--AVEAWLAEQQELWESRTDR 99
Query: 85 LDEFATQ 91
L++F T+
Sbjct: 100 LEQFVTE 106
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
pdb|3N3W|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Nuclease
Domain Ribonuclase Iii (Rnc) From Campylobacter Jejuni
Length = 248
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 443 YEFTEKGLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSSGSSKFVMHDLI 502
YEF +K L+ + ++S N+E++E LG +V +F + + + DL
Sbjct: 37 YEFKDKNLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAE----GDLS 92
Query: 503 HDFAELVSRETILRLEESTNLS 524
A LV+ ++ ++ S NL
Sbjct: 93 KLRAALVNEKSFAKIANSLNLG 114
>pdb|3O2R|A Chain A, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
pdb|3O2R|C Chain C, Structural Flexibility In Region Involved In Dimer
Formation Of Nuclease Domain Of Ribonuclase Iii (Rnc)
From Campylobacter Jejuni
Length = 170
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 443 YEFTEKGLIFLWMAGGIIRQSRNSEQMEDLGSKCFHDLVSRSIFQQTSSGSSKFVMHDLI 502
YEF +K L+ + ++S N+E++E LG +V +F + + + DL
Sbjct: 37 YEFKDKNLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEG----DLS 92
Query: 503 HDFAELVSRETILRLEESTNLS 524
A LV+ ++ ++ S NL
Sbjct: 93 KLRAALVNEKSFAKIANSLNLG 114
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
0.321 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,970,891
Number of Sequences: 62578
Number of extensions: 683773
Number of successful extensions: 1523
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1517
Number of HSP's gapped (non-prelim): 16
length of query: 661
length of database: 14,973,337
effective HSP length: 105
effective length of query: 556
effective length of database: 8,402,647
effective search space: 4671871732
effective search space used: 4671871732
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)