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= 025679
(249 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 33 DACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
+ C++CLE+F D + CKH FH +C+++W + CP+C P+
Sbjct: 16 ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3
Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4710b
Length = 91
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 23/42 (54%)
Query: 34 ACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C IC E+ + D +T C H FH CV W Q+S CP+C
Sbjct: 42 CCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C +C+ +F V C HEFH +CV +W + + CP+C
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC 66
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 6 MEEGKKPEDHMTSAAAFVEGGIQDSCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVL 63
+E+ K+ ++ M + V + D ++ C IC E F E+ +C H F C+
Sbjct: 25 LEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEA---VTLNCAHSFCSYCIN 81
Query: 64 EWCQRSSQCPMCWQPISLK 82
EW +R +CP+C + I K
Sbjct: 82 EWMKRKIECPICRKDIKSK 100
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 6 MEEGKKPEDHMTSAAAFVEGGIQDSCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVL 63
+E+ K+ ++ M + V + D ++ C IC E F E+ +C H F C+
Sbjct: 36 LEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEA---VTLNCAHSFCSYCIN 92
Query: 64 EWCQRSSQCPMCWQPISLK 82
EW +R +CP+C + I K
Sbjct: 93 EWMKRKIECPICRKDIKSK 111
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 38.1 bits (87), Expect = 0.004, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 33 DACSICLEEFSESDPSTV-TSCKHEFHLQCVLEWCQRSSQCPMCWQ 77
DAC C E + D V C H FH C+ W +++++CP+C Q
Sbjct: 27 DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQ 72
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 6 MEEGKKPEDHMTSAAAFVEGGIQDSCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVL 63
+E+ K+ ++ M + V + D ++ C IC E F E+ +C H F C+
Sbjct: 25 LEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEA---VTLNCAHSFCSYCIN 81
Query: 64 EWCQRSSQCPMCWQPISLK 82
EW +R +CP+C + I K
Sbjct: 82 EWMKRKIECPICRKDIKSK 100
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 12/53 (22%), Positives = 28/53 (52%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQ 87
C +C E+++ + C H FH C++ W ++ CP+C + ++ ++ +
Sbjct: 18 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 70
>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 = 33.9 bits (76), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPI 79
C ICLE+ S+ S C H F C+ W +++ CP+C P+
Sbjct: 8 CPICLED--PSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C+ICL E + C H FH CV +W + +CP+C
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPIC 57
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 35 CSICLEEFSESDPST-VTSCKHEFHLQCVLEWCQRSSQCPMC 75
C++CL E + + + + C H FH +CV W S CP+C
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49
>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 = 33.5 bits (75), Expect = 0.12, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 26 GIQDSCDDACSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISL 81
G++ S +C IC++ +SE + T C H F QC+ + + ++ CP C + I+
Sbjct: 4 GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 63
Query: 82 K 82
K
Sbjct: 64 K 64
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C +C F D +T+ C H F C++ + + S CP+C
Sbjct: 18 CVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 32.0 bits (71), Expect = 0.33, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 34 ACSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
+C IC++ +SE + T C H F QC+ + + ++ CP C + I+ K
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 57
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C +C F D +T+ C H F C++ + + S CP+C
Sbjct: 18 CVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger
And Chy Zinc Finger Domain-Containing Protein 1 From
Mus Musculus
Length = 55
Score = 31.6 bits (70), Expect = 0.43, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 30 SCDDACSICLEEFSESDP-STVTSCKHEFHLQCVLEWCQRSSQCPMCWQPIS 80
S C ICLE+ S + V C H H C E + +CP+C P S
Sbjct: 3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 31.2 bits (69), Expect = 0.51, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 34 ACSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
+C IC++ +SE + T C H F QC+ + + ++ CP C + I+ K
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
C +C F D +T+ C H F C++ + + S CP+C
Sbjct: 14 CVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPIC 52
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 31.2 bits (69), Expect = 0.57, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
CSIC D +T+T C H F C++ S++CP C
Sbjct: 18 CSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKC 56
>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 = 0.62, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 26 GIQDSCDDA--CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKD 83
+ + DD C IC E F+ + + C H + C+ ++ +QCP C ++ D
Sbjct: 14 AVMKTIDDLLRCGICFEYFNIA--MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD 71
Query: 84 ATSQELLEAVEQERSIRAN 102
+ +L+ + + + N
Sbjct: 72 LKNNRILDELVKSLNFARN 90
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 35 CSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLKDATSQELLEAVE 94
C IC + F VT C+H F C LE + + +C +C QP ++EL+ ++
Sbjct: 18 CFICRQAFQNP---VVTKCRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKELMAKLQ 74
Query: 95 Q 95
+
Sbjct: 75 K 75
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 32 DDACSICLEEFSESDPSTVTSCKHEFHLQCVLEWCQRSSQCPMC 75
++ C IC++ ++ + C H F +C+ +W R CP+C
Sbjct: 15 EEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPIC 54
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 34 ACSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
+C IC++ +SE + T C H F QC+ + + ++ CP C + I+ K
Sbjct: 9 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 61
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 34 ACSICLEEFSESDPS----TVTSCKHEFHLQCVLEWCQRSSQCPMCWQPISLK 82
+C IC++ +SE + T C H F QC+ + + ++ CP C + I+ K
Sbjct: 74 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 126
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 20/64 (31%)
Query: 32 DDACSICLEEFSESD------------PSTV---TSCKHEFHLQCVLE-WCQ----RSSQ 71
++ C IC+E+ + + P V T C H FHL C+L +C S Q
Sbjct: 25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84
Query: 72 CPMC 75
CP C
Sbjct: 85 CPSC 88
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
0.318 0.129 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,887,629
Number of Sequences: 62578
Number of extensions: 247084
Number of successful extensions: 512
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 480
Number of HSP's gapped (non-prelim): 42
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)