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= 000610
(1392 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 = 45.1 bits (105), Expect = 3e-04, Method: Composition-based stats.
Identities = 40/154 (25%), Positives = 57/154 (37%), Gaps = 34/154 (22%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPC-LTYIVNTTQACPYDGYLVTEADSKPLV 72
L +Y CP+C L+ EA+Q+ C H +CK C + I + CP D ++ E L
Sbjct: 15 LESKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE---NQLF 69
Query: 73 ESNKALAETIGKITVHCLFHRSGCTWQGPLSECTSHCSGCAFG----------------- 115
N A E + + V C GC + L H + C F
Sbjct: 70 PDNFAKREIL-SLMVKC--PNEGCLHKMELRHLEDHQAHCEFALMDCPQCQRPFQKFHIN 126
Query: 116 --------NSPVVCNRCAIQIVHRQVQEHAQNCP 141
V C+ CA + + H QNCP
Sbjct: 127 IHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCP 160
>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 = 40.8 bits (94), Expect = 0.005, Method: Composition-based stats.
Identities = 31/103 (30%), Positives = 45/103 (43%), Gaps = 9/103 (8%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPC-LTYIVNTTQACPYDGYLVTEADSKPLV 72
L +Y CP+C L+ EA+Q+ C H +CK C + I + CP D ++ E L
Sbjct: 15 LESKYECPIC--LMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE---NQLF 69
Query: 73 ESNKALAETIGKITVHCLFHRSGCTWQGPLSECTSHCSGCAFG 115
N A E + + V C GC + L H + C F
Sbjct: 70 PDNFAKREIL-SLMVKC--PNEGCLHKMELRHLEDHQAHCEFA 109
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 40.0 bits (92), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 12/98 (12%)
Query: 14 LAGEYFCPVCRLLVYPNEALQSQCTHLYCKPCLTYIVNT----TQACPYDGYLVTEADSK 69
L +Y C CR ++ Q+QC H YC CL I+++ AC ++G + E S
Sbjct: 28 LEAKYLCSACRNVL--RRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEG-IYEEGIS- 83
Query: 70 PLVESNKALAETIGKITVHCL---FHRSGCTWQGPLSE 104
++ES+ A + + V L GCTW+G L E
Sbjct: 84 -ILESSSAFPDNAARREVESLPAVCPSDGCTWKGTLKE 120
>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 = 0.063, 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 = 0.37, 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 = 31.6 bits (70), Expect = 3.0, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 20 CPVCRLLVYPNEALQ-SQCTHLYCKPCLTYIVNTTQACPYDGYLVTEADSKPLVESNKAL 78
C +C Y N A+ QC+H YC C+ ++ CP VTE D K +N+ L
Sbjct: 25 CGIC--FEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK----NNRIL 78
Query: 79 AETI 82
E +
Sbjct: 79 DELV 82
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 31.6 bits (70), Expect = 3.5, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 36 QCTHLYCKPCLTYIVNTTQACPYDGYLVTEADSKPL--VESNKALAETIGKI 85
+C H +CK C+ + T++ CP V + ++PL + S+K L + + K+
Sbjct: 33 ECLHSFCKTCIVRYLETSKYCPICDVQVHK--TRPLLNIRSDKTLQDIVYKL 82
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 31.6 bits (70), Expect = 3.5, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 36 QCTHLYCKPCLTYIVNTTQACPYDGYLVTEADSKPL--VESNKALAETIGKI 85
+C H +CK C+ + T++ CP V + ++PL + S+K L + + K+
Sbjct: 33 ECLHSFCKTCIVRYLETSKYCPICDVQVHK--TRPLLNIRSDKTLQDIVYKL 82
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 31.6 bits (70), Expect = 3.5, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 36 QCTHLYCKPCLTYIVNTTQACPYDGYLVTEADSKPL--VESNKALAETIGKI 85
+C H +CK C+ + T++ CP V + ++PL + S+K L + + K+
Sbjct: 29 ECLHSFCKTCIVRYLETSKYCPICDVQVHK--TRPLLNIRSDKTLQDIVYKL 78
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,546,225
Number of Sequences: 62578
Number of extensions: 1484420
Number of successful extensions: 2241
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2232
Number of HSP's gapped (non-prelim): 19
length of query: 1392
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1281
effective length of database: 8,027,179
effective search space: 10282816299
effective search space used: 10282816299
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)