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= 032328
(143 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 = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 29/48 (60%)
Query: 72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
V+C VCL G++ R LP C H FHA+C+D WL CP+CR V
Sbjct: 6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 49 SSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK 108
SS Q+P + + + S CVVC+ +F R+LP C H FHA+C+D WL
Sbjct: 2 SSGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59
Query: 109 TPICPICRTRVSPS 122
CPICR PS
Sbjct: 60 NRTCPICRADSGPS 73
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
S ++C VC E++ +G+ R LP C H FH CI WL + CP+CR ++
Sbjct: 14 SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
C +CL G+ R LP C H FH C+D WL+ CPICR +
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIE 62
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
C VCLE+F+ D+ + P C+H+FH +C+ WL +CP+C V
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 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 = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP 121
C +C + GD LP C H FH C+ WL K+ CP+CR P
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
+ + C++C E F + NC HSF + CI+ W+ + CPICR + ++L
Sbjct: 51 ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 106
Query: 129 KDG-----SSVSSDV 138
+ +++SS+V
Sbjct: 107 DNXINKMVNNLSSEV 121
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
+ + C++C E F + NC HSF + CI+ W+ + CPICR + ++L
Sbjct: 51 ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 106
Query: 129 KD 130
+
Sbjct: 107 DN 108
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
+ + C++C E F + NC HSF + CI+ W+ + CPICR + ++L
Sbjct: 62 ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 117
Query: 129 KD 130
+
Sbjct: 118 DN 119
>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 = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 10/62 (16%)
Query: 74 CVVCLE---NFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKD 130
C +CLE N+ M LP C H+F CI W+ + P CP+C+ V S V I D
Sbjct: 8 CPICLEDPSNYSMA-----LP-CLHAFCYVCITRWIRQNPTCPLCKVPVE-SVVHTIESD 60
Query: 131 GS 132
Sbjct: 61 SE 62
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 5/48 (10%)
Query: 73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
+C +C++ + L+ C HSF +CID W + CPICR +++
Sbjct: 17 ECCICMDG-----RADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 33.5 bits (75), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 68 GSSPVDCVVCLENF-RMGDKCRLL--PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
GS V C +C++ + + RL+ C H F +QC+ L CP CR +++ +
Sbjct: 4 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 63
Query: 125 GVILKDGSSVSSDVAIE 141
I +VS + ++
Sbjct: 64 HPIYIGSGTVSCPICMD 80
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 68 GSSPVDCVVCLENF-RMGDKCRLL--PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
GS V C +C++ + + RL+ C H F +QC+ L CP CR +++ +
Sbjct: 69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 127
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 116
>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 = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 97
>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 = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 107
>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 = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 105
>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 = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 105
>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 = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 89
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C H+FH CI WL +CP+ K G
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 99
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 24/52 (46%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
C+ C + D + C HSFH C+ W+ + CP+C+ ++G
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIG 80
>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 = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 67 RGSSPVDCVVCLENF-RMGDKCRLL--PNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
R S V C +C++ + + RL+ C H F +QC+ L CP CR +++
Sbjct: 6 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 62
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 29.6 bits (65), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 67 RGSSPVDCVVCLENF-RMGDKCRLL--PNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
R S V C +C++ + + RL+ C H F +QC+ L CP CR +++
Sbjct: 11 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 67
>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 = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
C +C E F + ++P C H++ + CI +L CP C V+
Sbjct: 25 CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT 68
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 72 VDCVVCLENF-RMGDKCRLL--PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVI 127
V C +C++ + + RL+ C H F +QC+ L CP CR +++ + I
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 62
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 92 NCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
C HSF CI +L + CPIC +V ++
Sbjct: 29 ECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 60
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 92 NCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
C HSF CI +L + CPIC +V ++
Sbjct: 33 ECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 93 CRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
C HSF CI +L + CPIC +V ++
Sbjct: 34 CLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64
>pdb|2LN0|A Chain A, Structure Of Moz
Length = 110
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRTR 118
C C + + D +C FH +C D L + P IC ICR R
Sbjct: 62 CSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPR 110
>pdb|3V43|A Chain A, Crystal Structure Of Moz
Length = 112
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRTR 118
C C + + D +C FH +C D L + P IC ICR R
Sbjct: 64 CSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPR 112
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
0.328 0.140 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,975,235
Number of Sequences: 62578
Number of extensions: 150028
Number of successful extensions: 315
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 276
Number of HSP's gapped (non-prelim): 46
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)