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= 033510
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 183 bits (465), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 85/88 (96%), Positives = 87/88 (98%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 30 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 89
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 90 FHCISRWLKTRQVCPLDNREWEFQKYGH 117
>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 = 183 bits (465), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 85/88 (96%), Positives = 87/88 (98%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 21 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 80
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 81 FHCISRWLKTRQVCPLDNREWEFQKYGH 108
>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 = 183 bits (464), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 85/88 (96%), Positives = 87/88 (98%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 19 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 78
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 79 FHCISRWLKTRQVCPLDNREWEFQKYGH 106
>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 = 182 bits (463), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 85/88 (96%), Positives = 87/88 (98%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 11 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 70
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 71 FHCISRWLKTRQVCPLDNREWEFQKYGH 98
>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 = 181 bits (460), Expect = 7e-47, Method: Compositional matrix adjust.
Identities = 85/88 (96%), Positives = 87/88 (98%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 3 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 62
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 63 FHCISRWLKTRQVCPLDNREWEFQKYGH 90
>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 = 180 bits (457), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 84/88 (95%), Positives = 86/88 (97%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KKW+AVALWAWDIVVDNCAICRNHI DLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 19 RFEVKKWNAVALWAWDIVVDNCAICRNHIXDLCIECQANQASATSEECTVAWGVCNHAFH 78
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 79 FHCISRWLKTRQVCPLDNREWEFQKYGH 106
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 171 bits (432), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 81/88 (92%), Positives = 83/88 (94%)
Query: 31 RFEIKKWSAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 90
RFE+KK +A A AWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH
Sbjct: 13 RFEVKKSNASAQSAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH 72
Query: 91 FHCISRWLKTRQVCPLDNSEWEFQKYGH 118
FHCISRWLKTRQVCPLDN EWEFQKYGH
Sbjct: 73 FHCISRWLKTRQVCPLDNREWEFQKYGH 100
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/76 (46%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 42 LWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR 101
+W+WD+ D CAICR +MD C+ CQA E+C V WG CNH+FH C+S W+K
Sbjct: 8 MWSWDVECDTCAICRVQVMDACLRCQAEN---KQEDCVVVWGECNHSFHNCCMSLWVKQN 64
Query: 102 QVCPLDNSEWEFQKYG 117
CPL +W Q+ G
Sbjct: 65 NRCPLCQQDWVVQRIG 80
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 18/24 (75%)
Query: 85 CNHAFHFHCISRWLKTRQVCPLDN 108
C HAFH C+ +WL+ R+VCPL N
Sbjct: 36 CKHAFHRKCLIKWLEVRKVCPLCN 59
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
CNH FH C+ +WLK + CP+
Sbjct: 44 CNHEFHAKCVDKWLKANRTCPI 65
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 19/47 (40%)
Query: 60 MDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 106
MD +EC A E C H FH C+ WL + CPL
Sbjct: 2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPL 48
>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 = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C HAF + CI+RW++ CPL
Sbjct: 24 CLHAFCYVCITRWIRQNPTCPL 45
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
CNH FH CI WL+ CP+
Sbjct: 36 CNHLFHDSCIVPWLEQHDSCPV 57
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 85 CNHAFHFHCISRWLKTRQVCPLDNSEWEFQ 114
C H FH C+ +WL T + CP+ + E Q
Sbjct: 35 CMHLFHQVCVDQWLITNKKCPICRVDIEAQ 64
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C+H FH C+S WL+ CP+
Sbjct: 61 CHHYFHKPCVSIWLQKSGTCPV 82
>pdb|2C53|A Chain A, A Comparative Study Of Uracil Dna Glycosylases From Human
And Herpes Simplex Virus Type 1
pdb|2C56|A Chain A, A Comparative Study Of Uracil Dna Glycosylases From Human
And Herpes Simplex Virus Type 1
Length = 244
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 72 SATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 107
S S V +G C H F +R+L+TR + P+D
Sbjct: 209 SNPSPLSKVPFGTCQH---FLVANRYLETRSISPID 241
>pdb|1UDI|E Chain E, Nucleotide Mimicry In The Crystal Structure Of The Uracil-
Dna Glycosylase-Uracil Glycosylase Inhibitor Protein
Complex
pdb|1LAU|E Chain E, Uracil-Dna Glycosylase
pdb|1UDG|A Chain A, The Structural Basis Of Specific Base Excision Repair By
Uracil-Dna Glycosylase
pdb|1UDH|A Chain A, The Structural Basis Of Specific Base Excision Repair By
Uracil-Dna Glycosylase
Length = 244
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 72 SATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 107
S S V +G C H F +R+L+TR + P+D
Sbjct: 209 SHPSPLSKVPFGTCQH---FLVANRYLETRSISPID 241
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F +CI+ W+K + CP+
Sbjct: 71 CAHSFCSYCINEWMKRKIECPI 92
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F +CI+ W+K + CP+
Sbjct: 71 CAHSFCSYCINEWMKRKIECPI 92
>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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F +CI+ W+K + CP+
Sbjct: 82 CAHSFCSYCINEWMKRKIECPI 103
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F CI R+L+T + CP+
Sbjct: 34 CLHSFCKTCIVRYLETSKYCPI 55
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F CI R+L+T + CP+
Sbjct: 30 CLHSFCKTCIVRYLETSKYCPI 51
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 85 CNHAFHFHCISRWLKTRQVCPL 106
C H+F CI R+L+T + CP+
Sbjct: 34 CLHSFCKTCIVRYLETSKYCPI 55
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
0.326 0.134 0.486
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,350,049
Number of Sequences: 62578
Number of extensions: 99125
Number of successful extensions: 301
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 278
Number of HSP's gapped (non-prelim): 24
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)