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= 017736
(367 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 58.2 bits (139), Expect = 8e-09, Method: Composition-based stats.
Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 13 KVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL-GC 71
++K L + C LC +ATTI CLH+FC+ CI L E + CP+C++ +
Sbjct: 2 RIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQVHKT 59
Query: 72 LPVEKLRPDHNLQDIRAKIFP------FKRRK 97
P+ +R D LQDI K+ P KRR+
Sbjct: 60 RPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRR 91
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 13 KVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL-GC 71
++K L + C LC +ATTI CLH+FC+ CI L E + CP+C++ +
Sbjct: 6 RIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQVHKT 63
Query: 72 LPVEKLRPDHNLQDIRAKIFP------FKRRK 97
P+ +R D LQDI K+ P KRR+
Sbjct: 64 RPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRR 95
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 13 KVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL-GC 71
++K L + C LC +ATTI CLH+FC+ CI L E + CP+C++ +
Sbjct: 6 RIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYL--ETSKYCPICDVQVHKT 63
Query: 72 LPVEKLRPDHNLQDIRAKIFP------FKRRK 97
P+ +R D LQDI K+ P KRR+
Sbjct: 64 RPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRR 95
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 12 VKVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDLGC 71
+ V +L + + CP+C +L+ T CLH FC CI L + CP C L
Sbjct: 44 IVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-CPTCRKKL-- 100
Query: 72 LPVEKLRPDHNLQDIRAKIFP 92
+ LRPD N + +KI+P
Sbjct: 101 VSKRSLRPDPNFDALISKIYP 121
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 12 VKVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDLGC 71
+ V +L + + CP+C +L+ T CLH FC CI L + CP C L
Sbjct: 43 IVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-CPTCRKKL-- 99
Query: 72 LPVEKLRPDHNLQDIRAKIFP 92
+ LRPD N + +KI+P
Sbjct: 100 VSKRSLRPDPNFDALISKIYP 120
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 12 VKVKRETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDLGC 71
+ V +L + + CP+C +L+ T CLH FC CI L + CP C L
Sbjct: 24 IVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-CPTCRKKL-- 80
Query: 72 LPVEKLRPDHNLQDIRAKIF 91
+ LRPD N + +KI+
Sbjct: 81 VSKRSLRPDPNFDALISKIY 100
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 23 MTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNI 67
+ C +C L +ATTI+ CLHTFC+ CI CP CNI
Sbjct: 16 ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNR--CPKCNI 58
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 10/69 (14%)
Query: 23 MTCPLCNSLLREATTISLCLHTFCRKCI---YE--KLSDEEADCCPVCNIDLGCLPVEKL 77
+TCP+C LL+E + C H+FCR CI YE + +D + + CPVC + P L
Sbjct: 20 VTCPICLELLKEPVSAD-CNHSFCRACITLNYESNRNTDGKGN-CPVCRVP---YPFGNL 74
Query: 78 RPDHNLQDI 86
+P+ ++ +I
Sbjct: 75 KPNLHVANI 83
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 23 MTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEA-------DCCPVCNIDLGCLPVE 75
+TCP+C LL E ++ C H+ CR CI +S++EA CPVC I E
Sbjct: 13 VTCPICLELLTEPLSLD-CGHSLCRACI--TVSNKEAVTSMGGKSSCPVCGIS---YSFE 66
Query: 76 KLRPDHNLQDI 86
L+ + +L +I
Sbjct: 67 HLQANQHLANI 77
>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 = 35.0 bits (79), Expect = 0.058, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 19 LEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCN 66
LE+ CP+C LREA + C H FC+ CI + + D CPV N
Sbjct: 15 LESKYECPICLMALREAVQ-TPCGHRFCKACIIKSIRD-AGHKCPVDN 60
>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 = 35.0 bits (79), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 17 ETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL 69
+ LE + C +C+ EA T++ C H+FC CI E + + CP+C D+
Sbjct: 59 DVLENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRKIE--CPICRKDI 108
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 34.7 bits (78), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 17 ETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL 69
+ LE + C +C+ EA T++ C H+FC CI E + + CP+C D+
Sbjct: 48 DVLENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRKIE--CPICRKDI 97
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 17 ETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL 69
+ LE + C +C+ EA T++ C H+FC CI E + + CP+C D+
Sbjct: 48 DVLENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMKRKIE--CPICRKDI 97
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 17 ETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVC 65
+ LE + C C ++LRE + C H FC C+ SD CPVC
Sbjct: 17 DRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCV----SDCIGTGCPVC 61
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 19 LEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADC----CPVC 65
L+ + CP+C +L++ TI C H FC KCI + E C CP+C
Sbjct: 17 LQEEVICPICLDILQKPVTID-CGHNFCLKCITQI---GETSCGFFKCPLC 63
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 19 LEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCN 66
LE+ CP+C LREA + C H FC+ CI + + D CPV N
Sbjct: 22 LESKYECPICLMALREAVQ-TPCGHRFCKACIIKSIRDAGHK-CPVDN 67
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 19 LEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADC----CPVC 65
L+ + CP+C +L++ TI C H FC KCI + E C CP+C
Sbjct: 17 LQEEVICPICLDILQKPVTID-CGHNFCLKCITQI---GETSCGFFKCPLC 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 17 ETLEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADC-CPVC 65
E L+ +C +C L+E I C H FC+ CI D E D CPVC
Sbjct: 10 ENLQVEASCSVCLEYLKEPVIIE-CGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|3ZTG|A Chain A, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
pdb|3ZTG|B Chain B, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
Length = 92
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 23 MTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCN 66
+ C +C ++ +A I C +++C +CI L + + CP C+
Sbjct: 14 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 31.2 bits (69), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 23 MTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCN 66
+ C +C ++ +A I C +++C +CI L + + CP C+
Sbjct: 16 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 25 CPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADC 61
CP+C LREA + C H FC+ CI + + D C
Sbjct: 9 CPICLMALREAVQ-TPCGHRFCKACIIKSIRDAGHKC 44
>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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 19 LEACMTCPLCNSLLREATTISLCLHTFCRKCIYEKLSDEEADC 61
LE+ CP+C LREA C H FC+ CI + + D C
Sbjct: 15 LESKYECPICLMALREAVQTP-CGHRFCKACIIKSIRDAGHKC 56
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 28 CNSLLREATTISLCLHTFCRKCIYEKLSDEEADCCPVCNIDL 69
C + A I C H+FC+KCI +K SD + CP+C + +
Sbjct: 19 CICMDGRADLILPCAHSFCQKCI-DKWSDRHRN-CPICRLQM 58
>pdb|2H3X|A Chain A, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dehydrogenase And Azurin From Alcaligenes
Faecalis (Form 3)
pdb|2H3X|D Chain D, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dehydrogenase And Azurin From Alcaligenes
Faecalis (Form 3)
pdb|2H47|A Chain A, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (Form 1)
pdb|2H47|D Chain D, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (Form 1)
pdb|2H47|F Chain F, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (Form 1)
pdb|2H47|H Chain H, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (Form 1)
pdb|2IAA|A Chain A, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (form 2)
pdb|2IAA|D Chain D, Crystal Structure Of An Electron Transfer Complex Between
Aromatic Amine Dephydrogenase And Azurin From
Alcaligenes Faecalis (form 2)
Length = 390
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 207 EAKADLWTPLNCLVEAANRTKSSKSNSQGPSLAKTDLHNFPDSEVFMPETKVKVELPNSP 266
E KA W P + +R P K H FP +E+++ +TK K + P
Sbjct: 274 EDKAKNWVPGGYNLVGLHRASGRMYVFMHPD-GKEGTHKFPAAEIWVMDTKTKQRVARIP 332
Query: 267 GGEICS 272
G + S
Sbjct: 333 GRDALS 338
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
0.313 0.129 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,949,645
Number of Sequences: 62578
Number of extensions: 358600
Number of successful extensions: 577
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 553
Number of HSP's gapped (non-prelim): 50
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
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: 52 (24.6 bits)