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= 000601
(1400 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 42.7 bits (99), Expect = 0.001, Method: Composition-based stats.
Identities = 40/162 (24%), Positives = 61/162 (37%), Gaps = 42/162 (25%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPC-LTYIVNTTQACPYDGYLVTEADSKVVL 72
L +Y CP+C L+ EA+Q+ C H +CK C + I + CP D++++L
Sbjct: 15 LESKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCP--------VDNEILL 64
Query: 73 SSAVVPLVESNKALAETIGKITVHCLFHRSGCTWQGPLSECTSHCSGCAFG--------- 123
+ + P N A E + + V C GC + L H + C F
Sbjct: 65 ENQLFP---DNFAKREIL-SLMVKC--PNEGCLHKMELRHLEDHQAHCEFALMDCPQCQR 118
Query: 124 ----------------NSPVVCNRCAIQIVHRQVQEHAQNCP 149
V C+ CA + + H QNCP
Sbjct: 119 PFQKFHINIHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCP 160
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 14/103 (13%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPCLTYIVNT----TQACPYDGYLVTEADSK 69
L +Y C CR ++ Q+QC H YC CL I+++ AC ++G + E
Sbjct: 28 LEAKYLCSACRNVL--RRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEG--IYEEGIS 83
Query: 70 VVLSSAVVPLVESNKALAETIGKITVHCLFHRSGCTWQGPLSE 112
++ SS+ P + A + + C GCTW+G L E
Sbjct: 84 ILESSSAFP----DNAARREVESLPAVC--PSDGCTWKGTLKE 120
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 38.9 bits (89), Expect = 0.022, Method: Composition-based stats.
Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 17/111 (15%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPC-LTYIVNTTQACPYDGYLVTEADSKVVL 72
L +Y CP+C L+ EA+Q+ C H +CK C + I + CP D++++L
Sbjct: 15 LESKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCP--------VDNEILL 64
Query: 73 SSAVVPLVESNKALAETIGKITVHCLFHRSGCTWQGPLSECTSHCSGCAFG 123
+ + P N A E + + V C GC + L H + C F
Sbjct: 65 ENQLFP---DNFAKREIL-SLMVKC--PNEGCLHKMELRHLEDHQAHCEFA 109
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 38.1 bits (87), Expect = 0.033, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPC-LTYIVNTTQACPYDGYLVTE 65
L +Y CP+C L+ EA+Q+ C H +CK C + I + CP D ++ E
Sbjct: 3 LGSKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE 53
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 37.4 bits (85), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPCLTY-IVNTTQACPYDGYLVTE 65
L +Y CP+C L+ EA+Q+ C H +CK C+ I + CP D ++ E
Sbjct: 22 LESKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE 72
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 34.7 bits (78), Expect = 0.38, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 20 CPVCRLLVYPNEALQSQCTHLYCKPCLTYIVNTTQA---CP 57
CP+C L+ E + ++C H++CK C+ ++N + CP
Sbjct: 24 CPICLELI--KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCP 62
>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure
pdb|2Y43|B Chain B, Rad18 Ubiquitin Ligase Ring Domain Structure
Length = 99
Score = 31.2 bits (69), Expect = 4.8, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 20 CPVCRLLVYPNEALQ-SQCTHLYCKPCLTYIVNTTQACPYDGYLVTEADSK 69
C +C Y N A+ QC+H YC C+ ++ CP VTE D K
Sbjct: 25 CGIC--FEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73
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
0.314 0.132 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,638,675
Number of Sequences: 62578
Number of extensions: 1484497
Number of successful extensions: 2256
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2247
Number of HSP's gapped (non-prelim): 16
length of query: 1400
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1289
effective length of database: 8,027,179
effective search space: 10347033731
effective search space used: 10347033731
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.9 bits)