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= 002752
(885 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 4.6, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 800 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 857
YY + +L K + Q HRK T FQR+ +P + + E Y Y +H+A+
Sbjct: 442 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 500
Query: 858 DDLQHGWCQRIKTEFTFEYNYLEDELI 884
++ C + F+ ++ + EL+
Sbjct: 501 ANMHKELCALM---FSLDWIKAKTELV 524
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 800 YYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVY--FDFHIAN 857
YY + +L K + Q HRK T FQR+ +P + + E Y Y +H+A+
Sbjct: 435 YYLHDLQVDFLTEKN-RSQLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMAS 493
Query: 858 DDLQHGWCQRIKTEFTFEYNYLEDELI 884
++ C + F+ ++ + EL+
Sbjct: 494 ANMHKELCALM---FSLDWIKAKTELV 517
>pdb|3QGD|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(2,
6-Dimethoxypyrimidin-4-Yl)-1-[(4-Ethylphenyl)sulfonyl]-
N-(4-Methoxybenzyl)piperazine-2-Carboxamide
pdb|3QGD|B Chain B, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(2,
6-Dimethoxypyrimidin-4-Yl)-1-[(4-Ethylphenyl)sulfonyl]-
N-(4-Methoxybenzyl)piperazine-2-Carboxamide
pdb|3QGE|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(2,
6-Dimethoxypyrimidin-4-Yl)-N-(4-Methoxybenzyl)-1-{[4-
(Trifluoromethoxy)phenyl]sulfonyl}piperazine-2-
Carboxamide
pdb|3QGE|B Chain B, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(2,
6-Dimethoxypyrimidin-4-Yl)-N-(4-Methoxybenzyl)-1-{[4-
(Trifluoromethoxy)phenyl]sulfonyl}piperazine-2-
Carboxamide
pdb|3QGF|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-
{[4-
(Trifluoromethoxy)phenyl]sulfonyl}piperazine-2-
Carboxamide
pdb|3QGF|B Chain B, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
(2r)-4-(6-Chloropyridazin-3-Yl)-N-(4-Methoxybenzyl)-1-
{[4-
(Trifluoromethoxy)phenyl]sulfonyl}piperazine-2-
Carboxamide
pdb|3QGG|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
N-Cyclopropyl-6-[(3r)-3-{[4-
(Trifluoromethoxy)benzyl]carbamoyl}-
4-{[4-(Trifluoromethoxy)phenyl]sulfonyl}piperazin-1-
Yl]pyridazine-3- Carboxamide
pdb|3QGG|B Chain B, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid And
N-Cyclopropyl-6-[(3r)-3-{[4-
(Trifluoromethoxy)benzyl]carbamoyl}-
4-{[4-(Trifluoromethoxy)phenyl]sulfonyl}piperazin-1-
Yl]pyridazine-3- Carboxamide
pdb|3Q0Z|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid
pdb|3Q0Z|B Chain B, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Complex With
(2e)-3-(4-{[(1-{[(13-Cyclohexyl-6-Oxo-6,7-
Dihydro-5h-Indolo[1,2-D][1,4]benzodiazepin-10-Yl)
Carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-
Enoic Acid
Length = 574
Score = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 32/107 (29%), Positives = 48/107 (44%), Gaps = 14/107 (13%)
Query: 58 YRDQIKTWIQSSEIKDKKALVDARKLIEREMERFKICEKETKTKAFSKEGLGQQPKTDPK 117
YRD +K E+K K + V A+ L E C+ A SK G G + +
Sbjct: 65 YRDVLK------EMKAKASTVKAKLLSVEEA-----CKLTPPHSARSKFGYGAKDVRNLS 113
Query: 118 EKAKSETRDWLNNLVSELESQID-SFEAELEGLTVK--KGKTRPPRL 161
KA + R +L+ + E+ ID + A+ E V+ KG +P RL
Sbjct: 114 SKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARL 160
>pdb|3FQL|A Chain A, Hepatitis C Virus Polymerase Ns5b (Con1 1-570) With
Hcv-796 Inhibitor
Length = 578
Score = 29.3 bits (64), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 32/107 (29%), Positives = 48/107 (44%), Gaps = 14/107 (13%)
Query: 58 YRDQIKTWIQSSEIKDKKALVDARKLIEREMERFKICEKETKTKAFSKEGLGQQPKTDPK 117
YRD +K E+K K + V A+ L E C+ A SK G G + +
Sbjct: 72 YRDVLK------EMKAKASTVKAKLLSVEEA-----CKLTPPHSARSKFGYGAKDVRNLS 120
Query: 118 EKAKSETRDWLNNLVSELESQID-SFEAELEGLTVK--KGKTRPPRL 161
KA + R +L+ + E+ ID + A+ E V+ KG +P RL
Sbjct: 121 SKAVNHIRSVWKDLLEDTETPIDTTIMAKNEVFCVQPEKGGRKPARL 167
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
0.311 0.129 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,174,429
Number of Sequences: 62578
Number of extensions: 959964
Number of successful extensions: 2080
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 2074
Number of HSP's gapped (non-prelim): 49
length of query: 885
length of database: 14,973,337
effective HSP length: 107
effective length of query: 778
effective length of database: 8,277,491
effective search space: 6439887998
effective search space used: 6439887998
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)