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= 028554
(207 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 26/45 (57%)
Query: 138 CPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPICDQVL 182
CP+C E+Y C H FH SCI+ W E+ +SCP+C + L
Sbjct: 18 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 116 ASPRKSEVSQLNVFAASEEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESC 175
+S +V +LN+ + C +CLE++ + I C+H FH C+++W E + C
Sbjct: 2 SSGSSGKVKELNL------HELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVC 55
Query: 176 PICDQVLIIL 185
P+C+ ++ L
Sbjct: 56 PLCNMPVLQL 65
>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 = 2e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 130 AASEEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
A +E CPIC EY + C H+FH C+ W ++S +CP+C
Sbjct: 35 GAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 134 EEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
E+ C +C+ ++++ + C H FH C+ +W + + +CPIC
Sbjct: 22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC 66
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 131 ASEEEDTCPICLEEY-DTENPKLITKCEHHFHLSCILEWNERSESCPICDQVLII 184
A ++ C +CL E D E + + +C H FH C+ W +CP+C +++
Sbjct: 1 AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 134 EEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
+E+ C IC++ LI C H F CI +W++R +CPIC
Sbjct: 14 DEEECCICMDG----RADLILPCAHSFCQKCIDKWSDRHRNCPIC 54
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 136 DTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
+ CPICLE D N + C H F CI W ++ +CP+C
Sbjct: 6 ERCPICLE--DPSNYSMALPCLHAFCYVCITRWIRQNPTCPLC 46
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 34.3 bits (77), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 138 CPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPICDQ 180
C IC + + +NP ++TKC H+F SC LE + C ICDQ
Sbjct: 18 CFICRQAF--QNP-VVTKCRHYFCESCALEHFRATPRCYICDQ 57
>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 = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 137 TCPICLEEYD--TENPKLI--TKCEHHFHLSCILEWNERSESCPICDQVL 182
+CPIC++ Y +N +LI T+C H F C+ + + + +CP C + +
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 130 AASEEEDTCPICLEEYD--TENPKLI--TKCEHHFHLSCILEWNERSESCPICDQVL 182
A +CPIC++ Y +N +LI T+C H F C+ + + + +CP C + +
Sbjct: 2 AMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 137 TCPICLEEYD--TENPKLI--TKCEHHFHLSCILEWNERSESCPICDQVL 182
+CPIC++ Y +N +LI T+C H F C+ + + + +CP C + +
Sbjct: 74 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 136 DTCPICLEEYDTENPKLIT-KCEHHFHLSCILEWNERSESCPICDQVLIILK 186
D C C E E+ ++ +C H FH C+ W +++ CP+C Q ++ +
Sbjct: 27 DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQR 78
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 137 TCPICLEEYD--TENPKLI--TKCEHHFHLSCILEWNERSESCPICDQVL 182
+CPIC++ Y +N +LI T+C H F C+ + + + +CP C + +
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 31.6 bits (70), Expect = 0.36, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 137 TCPICLEEYD--TENPKLI--TKCEHHFHLSCILEWNERSESCPIC 178
+CPIC++ Y +N +LI T+C H F C+ + + + +CP C
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 50
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.8 bits (68), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 153 ITKCEHHFHLSCILEWNERSESCPICD 179
I +C H F +CI+ + E S+ CPICD
Sbjct: 27 IIECLHSFCKTCIVRYLETSKYCPICD 53
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.8 bits (68), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 153 ITKCEHHFHLSCILEWNERSESCPICD 179
I +C H F +CI+ + E S+ CPICD
Sbjct: 31 IIECLHSFCKTCIVRYLETSKYCPICD 57
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 153 ITKCEHHFHLSCILEWNERSESCPICD 179
I +C H F +CI+ + E S+ CPICD
Sbjct: 31 IIECLHSFCKTCIVRYLETSKYCPICD 57
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERS---ESCPIC 178
+EE CPICL D + C H+F L CI + E S CP+C
Sbjct: 18 QEEVICPICL---DILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPICDQ 180
E E C IC EY E L C H F CI EW +R CPIC +
Sbjct: 51 ENELQCIIC-SEYFIEAVTL--NCAHSFCSYCINEWMKRKIECPICRK 95
>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 = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPICDQ 180
E E C IC EY E L C H F CI EW +R CPIC +
Sbjct: 62 ENELQCIIC-SEYFIEAVTL--NCAHSFCSYCINEWMKRKIECPICRK 106
>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 = 30.4 bits (67), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 131 ASEEEDTCPICLEEYDTENP-KLITKCEHHFHLSCILEWNERSESCPICD 179
S CPICLE+ T + C H H +C E + CP+C
Sbjct: 1 GSSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
E E C IC EY E L C H F CI EW +R CPIC
Sbjct: 51 ENELQCIIC-SEYFIEAVTL--NCAHSFCSYCINEWMKRKIECPIC 93
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 29.6 bits (65), Expect = 1.3, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERS---ESCPIC 178
+EE CPICL D + C H+F L CI + E S CP+C
Sbjct: 18 QEEVICPICL---DILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 8/67 (11%)
Query: 115 IASPRKSEVSQLNVFAASEEEDTCPICLEEYDTENPKLITKCEHHFHLSCILE-WNERS- 172
+++ R EV NV A ++ CPICLE + P + TKC+H F C+L+ N++
Sbjct: 3 LSALRVEEVQ--NVINAMQKILECPICLEL--IKEP-VSTKCDHIFCKFCMLKLLNQKKG 57
Query: 173 -ESCPIC 178
CP+C
Sbjct: 58 PSQCPLC 64
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 135 EDTCPICLEEYDTENPKLITKCEHHFHLSCILEWN---ERSESCPIC 178
E +C +CLE Y E +I +C H+F +CI W ER CP+C
Sbjct: 15 EASCSVCLE-YLKE--PVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 138 CPICLEEYDTENPKLITKCEHHFHLSCILEWNERSESCPIC 178
C ICL + C H FH C+ +W ++ CPIC
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPIC 57
>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 = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 128 VFAASEEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERS------ESCPIC 178
+ +EE TCPICLE L C H F +C+ +++S SCP+C
Sbjct: 12 ILVNVKEEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVC 65
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 135 EDTCPICLEEYDTENP-KLITKCEHHFHLSCILEWNERSESCPIC 178
+ CPICLE+ T + C H H +C E + CP+C
Sbjct: 5 QQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 20/67 (29%)
Query: 135 EDTCPICLEEY-------DTENPKLI--------TKCEHHFHLSCILEW-----NERSES 174
E+ C IC+E+ D + K + TKC H FHL C+L + S
Sbjct: 25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84
Query: 175 CPICDQV 181
CP C +
Sbjct: 85 CPSCKTI 91
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 133 EEEDTCPICLEEYDTENPKLITKCEHHFHLSCILEWNERS-------ESCPICD 179
+EE TCPICLE L C H +CI N+ + SCP+C
Sbjct: 10 QEEVTCPICLELL---TEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCG 60
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 9/57 (15%)
Query: 128 VFAASEEEDTCPICLEEYDTENPKLITKCEHHFHLSCI---LEWNERSE---SCPIC 178
V +EE TCPICLE + C H F +CI E N ++ +CP+C
Sbjct: 12 VLEMIKEEVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVC 65
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
0.320 0.135 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,814,339
Number of Sequences: 62578
Number of extensions: 195237
Number of successful extensions: 467
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 433
Number of HSP's gapped (non-prelim): 52
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)