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= 005608
(688 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 = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 643 CAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSIT 688
C +C ++ ++G+S+R LPC H FH CI PWL + SCPVC+ S+T
Sbjct: 18 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLT 63
>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 = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 621 ASANQINSLPLSTVQTDNF----EEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSR 676
AS I++LP V D+ E C IC GD LPC H FHK C+ WL +
Sbjct: 17 ASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK 76
Query: 677 RPSCPVCK 684
+CPVC+
Sbjct: 77 SGTCPVCR 84
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 20/45 (44%), Positives = 27/45 (60%)
Query: 643 CAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
C ICL G+ +R LPC+H FH+ C+D WL CP+C+ I
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDI 61
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 50.8 bits (120), Expect = 3e-06, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 643 CAICLDNPSIGDSIRHLP-CLHKFHKDCIDPWLSRRPSCPVCKSSI 687
CA+CL G+ R LP C H FH +C+D WL +CP+C+ ++
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53
>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 = 50.8 bits (120), Expect = 3e-06, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 641 EACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
E C ICL++PS + LPCLH F CI W+ + P+CP+CK +
Sbjct: 6 ERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 634 VQTDNFEEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
V+ N E CA+CL++ D + PC H FH+ C+ WL R CP+C +
Sbjct: 9 VKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 619 SGASANQINSLPLSTVQTDNFEEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRP 678
S S+ Q+ S + + + C +C+ + +R LPC H+FH C+D WL
Sbjct: 2 SSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR 61
Query: 679 SCPVCKS 685
+CP+C++
Sbjct: 62 TCPICRA 68
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 640 EEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSIT 688
EE C IC+D G + LPC H F + CID W R +CP+C+ +T
Sbjct: 15 EEECCICMD----GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 36.2 bits (82), Expect = 0.071, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 640 EEACAICLDNPSIGDSIRH-LPCLHKFHKDCIDPWLSRRPSCPVCKSS 686
++ C ICL++ + H LPC H H+ C + L CP+C S
Sbjct: 5 QQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS 52
>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 = 35.8 bits (81), Expect = 0.086, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 659 LPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
L C H F CI+ W+ R+ CP+C+ I
Sbjct: 80 LNCAHSFCSYCINEWMKRKIECPICRKDI 108
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 659 LPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
L C H F CI+ W+ R+ CP+C+ I
Sbjct: 69 LNCAHSFCSYCINEWMKRKIECPICRKDI 97
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 659 LPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
L C H F CI+ W+ R+ CP+C+ I
Sbjct: 69 LNCAHSFCSYCINEWMKRKIECPICRKDI 97
>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 = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 642 ACAICLDNPSIGDSIRH-LPCLHKFHKDCIDPWLSRRPSCPVC 683
C ICL++ + H LPC H H+ C + L CP+C
Sbjct: 7 GCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 640 EEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWL-SRRPSCPVCKSSIT 688
E C ICLD + +++ CLH+F DCI L S CP C+ +
Sbjct: 54 ELMCPICLD--MLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 640 EEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWL-SRRPSCPVCKSSI 687
E C ICLD + +++ CLH+F DCI L S CP C+ +
Sbjct: 34 ELMCPICLD--MLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKL 80
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 654 DSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
D+ + CLH F K CI +L CP+C +
Sbjct: 23 DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 56
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 640 EEACAICLDNPSIGDSIRHLPCLHKFHKDCIDPWL-SRRPSCPVCKSSIT 688
E C ICLD + +++ CLH+F DCI L S CP C+ +
Sbjct: 53 ELMCPICLD--MLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 100
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 654 DSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
D+ + CLH F K CI +L CP+C +
Sbjct: 27 DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 654 DSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
D+ + CLH F K CI +L CP+C +
Sbjct: 27 DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60
>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 = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>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 = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL 86
>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 = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>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 = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 643 CAICLDNPSIGDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSIT 688
C IC + +I I C H + CI +LS + CP C ++T
Sbjct: 25 CGICFEYFNIAMIIPQ--CSHNYCSLCIRKFLSYKTQCPTCCVTVT 68
>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 = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>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 = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 661 CLHKFHKDCIDPWLSRRPSCPV 682
C H FH CI WL R CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 28.9 bits (63), Expect = 9.1, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 642 ACAICLDNPSI----GDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
+C IC+D S G I C H F C+ L +CP C+ I
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.9 bits (63), Expect = 9.7, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 642 ACAICLDNPSI----GDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
+C IC+D S G I C H F C+ L +CP C+ I
Sbjct: 9 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58
Score = 28.9 bits (63), Expect = 9.7, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 642 ACAICLDNPSI----GDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
+C IC+D S G I C H F C+ L +CP C+ I
Sbjct: 74 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123
>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 = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 642 ACAICLDNPSI----GDSIRHLPCLHKFHKDCIDPWLSRRPSCPVCKSSI 687
+C IC+D S G I C H F C+ L +CP C+ I
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
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 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,387,624
Number of Sequences: 62578
Number of extensions: 689250
Number of successful extensions: 1107
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1080
Number of HSP's gapped (non-prelim): 38
length of query: 688
length of database: 14,973,337
effective HSP length: 105
effective length of query: 583
effective length of database: 8,402,647
effective search space: 4898743201
effective search space used: 4898743201
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: 55 (25.8 bits)