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= 002863
(873 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 = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 326 DIPELAETLAKDCGGLPLALITVGRAMASRKTPREWEHAIEVLRSSASK 374
D+PE A ++ K+C G PL + +G + R P WE+ ++ L++ K
Sbjct: 305 DLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQNKQFK 351
>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 = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 325 PDIPELAETLAKDCGGLPLALITVGRAMASRKTPREWEHAIEVLRSSASK 374
D+PE A ++ K+C G PL + +G + R P WE+ ++ L++ K
Sbjct: 310 ADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQNKQFK 357
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 34.3 bits (77), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 549 KSMASLRVLKLSH---SDLPCEISNLVSLQYLDLSNSIPDRLPLGLKYLVNLKCLNLE 603
K++++LRVL LSH + LP E+ + L+Y +++ LP L NL+ L +E
Sbjct: 267 KNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVE 324
>pdb|4FHO|A Chain A, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
pdb|4FHO|B Chain B, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
Length = 231
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 37/138 (26%), Positives = 66/138 (47%), Gaps = 14/138 (10%)
Query: 493 GLTEAPSVGMWKDVTRMSLMDNKIKRLTVSPTSPRLLTLFLNSNYFKNDKVNYHFFKSMA 552
G+T + ++ + L DN+I LT ++ L L+ N KN +
Sbjct: 58 GVTTIEGIQYLNNLIGLELKDNQITDLTPLKNLTKITELELSGNPLKNVSA----IAGLQ 113
Query: 553 SLRVLKLSHSDLP--CEISNLVSLQ--YLDLSNSIPDRLPLGLKYLVNLKCLNLEYTFRL 608
S++ L L+ + + ++ L +LQ YLDL N I + PL L NL+ L++ ++
Sbjct: 114 SIKTLDLTSTQITDVTPLAGLSNLQVLYLDL-NQITNISPLA--GLTNLQYLSIGNN-QV 169
Query: 609 SRISPQVISNLKMLRVLR 626
+ ++P ++NL L LR
Sbjct: 170 NDLTP--LANLSKLTTLR 185
>pdb|1IHG|A Chain A, Bovine Cyclophilin 40, Monoclinic Form
pdb|1IIP|A Chain A, Bovine Cyclophilin 40, Tetragonal Form
Length = 370
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 287 EVCGQMEAHRSFKVEC--LRYDDAWKLFELKVGADTLDSHPDIPELAETLAKD 337
EV G+ A EC L+ D W +F K G+ DSHPD PE A+ KD
Sbjct: 166 EVKGEKPAKLCVIAECGELKEGDDWGIFP-KDGSG--DSHPDFPEDADVDLKD 215
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 326 DIPELAETLAKDCGGLPLALITVGRAMASRKTPREWEHAIEVLRSSASK 374
D+P A ++ K+C G PL + +G + R P W + + L++ K
Sbjct: 305 DLPAEAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYYLRQLQNKQFK 351
>pdb|2J5C|A Chain A, Rational Conversion Of Substrate And Product Specificity
In A Monoterpene Synthase. Structural Insights Into The
Molecular Basis Of Rapid Evolution.
pdb|2J5C|B Chain B, Rational Conversion Of Substrate And Product Specificity
In A Monoterpene Synthase. Structural Insights Into The
Molecular Basis Of Rapid Evolution
Length = 569
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 10/81 (12%)
Query: 472 ALWIASTMDN-----KKEKFLVLTGAGLTEAPSVGMWKDVT---RMSLMDNKIKRLTVSP 523
LW ST+ + K+EK L + AG+ + + + ++V R+ L+D+ ++RL +S
Sbjct: 43 TLWDFSTIQSFDSEYKEEKHL-MRAAGMIDQVKMMLQEEVDSIRRLELIDD-LRRLGISC 100
Query: 524 TSPRLLTLFLNSNYFKNDKVN 544
R + LNS Y+ N++++
Sbjct: 101 HFEREIVEILNSKYYTNNEID 121
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 29.3 bits (64), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 326 DIPELAETLAKDCGGLPLALITVGRAMASRKTPREWEHAIEVLRSSASK 374
D+P A ++ K+C G PL + +G + R P W + + L++ K
Sbjct: 312 DLPAEAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYYLRQLQNKQFK 358
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
0.323 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,593,090
Number of Sequences: 62578
Number of extensions: 904429
Number of successful extensions: 1867
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 1828
Number of HSP's gapped (non-prelim): 77
length of query: 873
length of database: 14,973,337
effective HSP length: 107
effective length of query: 766
effective length of database: 8,277,491
effective search space: 6340558106
effective search space used: 6340558106
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (26.2 bits)