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= 045579
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI 99
C +CL DGE R P C FH+ C+D WL H TCP+CR++ +
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 44 QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
+E S C +C E++ GES R P C +FH CI WL++H +CPVCR S
Sbjct: 9 EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKS 61
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/50 (48%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE 102
C ICL +GE R P C +FH VC+DQWL + CP+CR +DIE
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR---VDIE 62
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 28 GDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE 87
G +P ++ CV+C+ +F + R+ P C FH+ C+D+WLK
Sbjct: 1 GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59
Query: 88 HLTCPVCRI 96
+ TCP+CR
Sbjct: 60 NRTCPICRA 68
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
C IC +V G+ P C+ FH C+ WL++ TCPVCR
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
C+IC E F++ + C F S CI++W+K + CP+CR
Sbjct: 56 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICR 94
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
C+IC E F++ + C F S CI++W+K + CP+CR
Sbjct: 67 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICR 105
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
C+IC E F++ + C F S CI++W+K + CP+CR
Sbjct: 56 CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICR 94
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI 96
C IC++ D L C F CID+W H CP+CR+
Sbjct: 18 CCICMDGRAD-----LILPCAHSFCQKCIDKWSDRHRNCPICRL 56
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI 101
C +CLE+F + + P C FH C+ +WL+ CP+C + + +
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQL 65
>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 = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI 96
M + C ICLE D + + C F VCI +W++++ TCP+C++
Sbjct: 1 MATVAERCPICLE---DPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKV 48
>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 = 0.27, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%)
Query: 49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVC 94
S+ C ICLE+ C + H C ++ LKE CP+C
Sbjct: 4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 21/49 (42%)
Query: 49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
S C ICLE+ C + H C ++ LKE CP+C S
Sbjct: 4 SQQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS 52
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 69 FPVCYRIFHSVCIDQWLKEHLTCPV 93
+ VC FH CI +WLK CP+
Sbjct: 81 WGVCNHAFHFHCISRWLKTRQVCPL 105
>pdb|3LRQ|A Chain A, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|B Chain B, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|C Chain C, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|D Chain D, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d
Length = 100
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLT-CPVCR 95
C IC E D RL P C ++ CI +WL E CP CR
Sbjct: 25 CFICXEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCR 65
>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 108
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 53 CVICLENFVDG--ESCRL-FPVCYRIFHSVCIDQWLKEHLTCPV 93
C+ C N E C + + VC FH CI +WLK CP+
Sbjct: 53 CIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 96
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 53 CVICLENFVDG--ESCRL-FPVCYRIFHSVCIDQWLKEHLTCPV 93
C+ C N E C + + VC FH CI +WLK CP+
Sbjct: 51 CIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 28.5 bits (62), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 53 CVICLENFVDG--ESCRL-FPVCYRIFHSVCIDQWLKEHLTCPV 93
C+ C N E C + + VC FH CI +WLK CP+
Sbjct: 51 CIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 53 CVICLENFVDG--ESCRL-FPVCYRIFHSVCIDQWLKEHLTCPV 93
C+ C N E C + + VC FH CI +WLK CP+
Sbjct: 45 CIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 88
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp
Abasic Site Containing Dna-Duplex
Length = 98
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 69 FPVCYRIFHSVCIDQWLKEHLTCPV 93
+ VC FH CI +WLK CP+
Sbjct: 62 WGVCNHAFHFHCISRWLKTRQVCPL 86
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 69 FPVCYRIFHSVCIDQWLKEHLTCPV 93
+ VC FH CI +WLK CP+
Sbjct: 54 WGVCNHAFHFHCISRWLKTRQVCPL 78
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 68 LFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
++ C FH+ C+ W+K++ CP+C+
Sbjct: 44 VWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
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
0.325 0.141 0.470
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,862,923
Number of Sequences: 62578
Number of extensions: 103556
Number of successful extensions: 229
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 197
Number of HSP's gapped (non-prelim): 41
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)