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= 008905
(549 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 42.0 bits (97), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDC-FKRCPLC 159
V CPICL+ P CGH FC CI Q +G+ C F +CPLC
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCITQ---IGET----SCGFFKCPLC 63
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDC-FKRCPLC 159
V CPICL+ P CGH FC CI Q +G+ C F +CPLC
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCITQ---IGET----SCGFFKCPLC 63
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCI-LQYLLMGDEDYKGDCFKRCPLCFVMISSKELY 169
V CPICLE P C H FC CI L Y + D KG+ CP+C V L
Sbjct: 20 VTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGN----CPVCRVPYPFGNLK 75
Query: 170 -TIHIENV 176
+H+ N+
Sbjct: 76 PNLHVANI 83
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 109 LSVQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLC 159
+ C +CLEY P I CGH FC CI ++ + D+ CP+C
Sbjct: 14 VEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFP------CPVC 58
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 37.4 bits (85), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLC 159
++CPICLE P T C HIFC C+L+ L KG +CPLC
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLL----NQKKGP--SQCPLC 64
>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
Resonance Spectroscopy; A New Structural Class Of Zinc-
Finger
Length = 68
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 112 QCPICLEYPLCPQIT-SCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISS 165
+CPICLE P + C H FC+ CI +++ CPLC V + S
Sbjct: 7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQN---------PTCPLCKVPVES 52
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 112 QCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLC 159
+C ICL+ + P C H+FC+ C+ +G KRC LC
Sbjct: 17 ECAICLQTCVHPVSLPCKHVFCYLCVKGASWLG---------KRCALC 55
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 34.3 bits (77), Expect = 0.20, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 110 SVQCPICLE-YPLCPQ------ITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVM 162
+V CPIC++ Y Q T CGH+FC C+ L + CP C
Sbjct: 7 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT---------CPTCRKK 57
Query: 163 ISSKELYTIHI 173
I+ K + I+I
Sbjct: 58 INHKRYHPIYI 68
Score = 34.3 bits (77), Expect = 0.20, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 110 SVQCPICLE-YPLCPQ------ITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVM 162
+V CPIC++ Y Q T CGH+FC C+ L + CP C
Sbjct: 72 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT---------CPTCRKK 122
Query: 163 ISSKELYTIHI 173
I+ K + I+I
Sbjct: 123 INHKRYHPIYI 133
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 33.9 bits (76), Expect = 0.22, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 110 SVQCPICLE-YPLCPQ------ITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVM 162
+V CPIC++ Y Q T CGH+FC C+ L + CP C
Sbjct: 10 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT---------CPTCRKK 60
Query: 163 ISSKELYTIHI 173
I+ K + I+I
Sbjct: 61 INHKRYHPIYI 71
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.5 bits (75), Expect = 0.30, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 16/70 (22%)
Query: 111 VQCPICLE-YPLCPQ------ITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMI 163
V CPIC++ Y Q T CGH+FC C+ L + CP C I
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANT---------CPTCRKKI 54
Query: 164 SSKELYTIHI 173
+ K + I+I
Sbjct: 55 NHKRYHPIYI 64
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 33.5 bits (75), Expect = 0.32, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSKELYT 170
+QC IC EY + +C H FC CI +++ E CP+C I SK Y+
Sbjct: 65 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE---------CPICRKDIKSKT-YS 114
Query: 171 IHIEN 175
+ ++N
Sbjct: 115 LVLDN 119
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 33.1 bits (74), Expect = 0.39, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSKELY- 169
V CPICLE P CGH C CI G CP+C + S + L
Sbjct: 13 VTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGK--SSCPVCGISYSFEHLQA 70
Query: 170 TIHIENV 176
H+ N+
Sbjct: 71 NQHLANI 77
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSKELYT 170
+QC IC EY + +C H FC CI +++ E CP+C I SK Y+
Sbjct: 54 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE---------CPICRKDIKSKT-YS 103
Query: 171 IHIEN 175
+ ++N
Sbjct: 104 LVLDN 108
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSKELYT 170
+QC IC EY + +C H FC CI +++ E CP+C I SK Y+
Sbjct: 54 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE---------CPICRKDIKSKT-YS 103
Query: 171 IHIEN 175
+ ++N
Sbjct: 104 LVLDN 108
>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 = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 103 VRYSNPLS--VQCPICLEYPLCPQITSCGHIFCFPCILQ 139
V + PL +CPICL T CGH FC CI++
Sbjct: 9 VEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIK 47
>pdb|4E51|A Chain A, Crystal Structure Of A Histidyl-Trna Synthetase Hisrs From
Burkholderia Thailandensis Bound To Histidine
pdb|4E51|B Chain B, Crystal Structure Of A Histidyl-Trna Synthetase Hisrs From
Burkholderia Thailandensis Bound To Histidine
Length = 467
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 425 TEIKDKDSYNFYQAIDGQHLILHPLNLKCLLHHYGSYDML---PHRI 468
T+I +K+ Y+F A++G++L L P N ++ ++ML P R+
Sbjct: 87 TDIVEKEMYSFVDALNGENLTLRPENTAAVVRAAIEHNMLYDGPKRL 133
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 111 VQCPICLEYPLCPQITS-CGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSK 166
+ CPICL+ T C H FC CI+ L G+ K CP C + SK
Sbjct: 55 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGN--------KECPTCRKKLVSK 103
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 112 QCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPL 158
+CPICL T CGH FC CI++ + D +CP+
Sbjct: 8 ECPICLMALREAVQTPCGHRFCKACIIKSIR--------DAGHKCPV 46
>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 = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 103 VRYSNPLS--VQCPICLEYPLCPQITSCGHIFCFPCILQ 139
V + PL +CPICL T CGH FC CI++
Sbjct: 9 VEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIK 47
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 107 NPLSVQCPICLEYPL-CPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMI-S 164
NP + C +C Y + I C H FC CI++YL + K CP+C V +
Sbjct: 9 NP-HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL---------ETSKYCPICDVQVHK 58
Query: 165 SKELYTIHIENVRQHAV 181
++ L I + Q V
Sbjct: 59 TRPLLNIRSDKTLQDIV 75
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 107 NPLSVQCPICLEYPL-CPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMI-S 164
NP + C +C Y + I C H FC CI++YL + K CP+C V +
Sbjct: 13 NP-HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL---------ETSKYCPICDVQVHK 62
Query: 165 SKELYTIHIENVRQHAV 181
++ L I + Q V
Sbjct: 63 TRPLLNIRSDKTLQDIV 79
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 107 NPLSVQCPICLEYPL-CPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMI-S 164
NP + C +C Y + I C H FC CI++YL + K CP+C V +
Sbjct: 13 NP-HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL---------ETSKYCPICDVQVHK 62
Query: 165 SKELYTIHIENVRQHAV 181
++ L I + Q V
Sbjct: 63 TRPLLNIRSDKTLQDIV 79
>pdb|2LDR|A Chain A, Solution Structure Of Helix-Ring Domain Of Cbl-B In The
Tyr363 Phosphorylated Form
Length = 82
Score = 29.6 bits (65), Expect = 4.3, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 113 CPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFVMISSKE 167
C IC E +I CGH+ C C+ + + D +G CP C I E
Sbjct: 29 CKICAENDKDVKIEPCGHLMCTSCLTAW---QESDGQG-----CPFCRCEIKGTE 75
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 111 VQCPICLEYPLCPQITSCGHIFCFPCI 137
V CPICLE P CGH FC C+
Sbjct: 20 VTCPICLELLTQPLSLDCGHSFCQACL 46
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 29.3 bits (64), Expect = 6.5, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 112 QCPICLEYPLCPQITSCGHIFCFPCILQYLLMGDEDYKGDCFKRCPLCFV 161
+C IC + P +T C H FC C L++ F+ P C++
Sbjct: 17 RCFICRQAFQNPVVTKCRHYFCESCALEH------------FRATPRCYI 54
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 103 VRYSNPLS--VQCPICLEYPLCPQITSCGHIFCFPCILQYL 141
V + PL +CPICL T CGH FC CI++ +
Sbjct: 16 VEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSI 56
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
0.316 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,557,522
Number of Sequences: 62578
Number of extensions: 621678
Number of successful extensions: 1250
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 1228
Number of HSP's gapped (non-prelim): 48
length of query: 549
length of database: 14,973,337
effective HSP length: 104
effective length of query: 445
effective length of database: 8,465,225
effective search space: 3767025125
effective search space used: 3767025125
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)