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= 046929
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 179 DVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPIC 221
++C CL+++ P + C H FH C+ +WLE + CP+C
Sbjct: 16 ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 154 SESSDKALATKAAYGPYTQTSTEDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLE 213
E +K A K + E+E C C EY E +T C+H F CI EW++
Sbjct: 29 KEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIE--AVTLNCAHSFCSYCINEWMK 85
Query: 214 RSESCPICGKEME 226
R CPIC K+++
Sbjct: 86 RKIECPICRKDIK 98
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 154 SESSDKALATKAAYGPYTQTSTEDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLE 213
E +K A K + E+E C C EY E +T C+H F CI EW++
Sbjct: 29 KEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIE--AVTLNCAHSFCSYCINEWMK 85
Query: 214 RSESCPICGKEME 226
R CPIC K+++
Sbjct: 86 RKIECPICRKDIK 98
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%)
Query: 181 CPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPICGKEM 225
CP C ++Y C+H FH CI WLE+ +SCP+C K +
Sbjct: 18 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 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 = 2e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 174 STEDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPIC 221
+ E CP C EY + C H+FH C+ WL++S +CP+C
Sbjct: 36 AVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVC 83
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 154 SESSDKALATKAAYGPYTQTSTEDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLE 213
E +K A K + E+E C C EY E +T C+H F CI EW++
Sbjct: 40 KEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIE--AVTLNCAHSFCSYCINEWMK 96
Query: 214 RSESCPICGKEME 226
R CPIC K+++
Sbjct: 97 RKIECPICRKDIK 109
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 177 DEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPIC 221
++ +C C+ ++ C+H FH C+ +WL+ + +CPIC
Sbjct: 22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC 66
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 37.0 bits (84), Expect = 0.009, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 174 STEDEDVCPTCLDEYTP-ENPKITTRCSHHFHLGCIYEWLERSESCPIC 221
+ +D C CL E E + RC H FH C+ WL +CP+C
Sbjct: 1 AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 181 CPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPICGKEME 226
CP CL++ P N + C H F CI W+ ++ +CP+C +E
Sbjct: 8 CPICLED--PSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51
>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 = 35.0 bits (79), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPLDNREWEF 103
>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 = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNREWEF 101
>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 = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPLDNREWEF 101
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 34.7 bits (78), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPLDNREWEF 95
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 34.7 bits (78), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPLDNREWEF 112
>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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPLDNREWEF 93
>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 = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEMEF 227
C+H FH CI WL+ + CP+ +E EF
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPLDNREWEF 85
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 177 DEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERSESCPICGKEM 225
DE+ C C+D + C+H F CI +W +R +CPIC +M
Sbjct: 14 DEEECCICMDGRA----DLILPCAHSFCQKCIDKWSDRHRNCPICRLQM 58
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 181 CPTCLDEYT--PENPK--ITTRCSHHFHLGCIYEWLERSESCPICGKEM 225
CP C+D Y+ +N + ++T C H F C+ + L+ + +CP C K++
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEME 226
C H FH C+ +WL ++ CPIC ++E
Sbjct: 35 CMHLFHQVCVDQWLITNKKCPICRVDIE 62
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
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: 181 CPTCLDEYT--PENPK--ITTRCSHHFHLGCIYEWLERSESCPICGKEME 226
CP C+D Y+ +N + ++T C H F C+ + L+ + +CP C K++
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59
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: 181 CPTCLDEYT--PENPK--ITTRCSHHFHLGCIYEWLERSESCPICGKEME 226
CP C+D Y+ +N + ++T C H F C+ + L+ + +CP C K++
Sbjct: 75 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 124
>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 = 0.22, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 181 CPTCLDEYT--PENPK--ITTRCSHHFHLGCIYEWLERSESCPICGKEME 226
CP C+D Y+ +N + ++T C H F C+ + L+ + +CP C K++
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 62
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 181 CPTCLDEYT--PENPK--ITTRCSHHFHLGCIYEWLERSESCPICGKEM 225
CP C+D Y+ +N + ++T C H F C+ + L+ + +CP C K++
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 30.8 bits (68), Expect = 0.70, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 176 EDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERS---ESCPIC 221
++E +CP CLD + P +T C H+F L CI + E S CP+C
Sbjct: 18 QEEVICPICLD--ILQKP-VTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 30.4 bits (67), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 179 DVCPTCLDEYTPENPKITT-RCSHHFHLGCIYEWLERSESCPICGKE 224
D C C E E+ + C+H FH C+ W++++ CP+C ++
Sbjct: 27 DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 30.0 bits (66), Expect = 1.0, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 176 EDEDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEWLERS---ESCPIC 221
++E +CP CLD + P +T C H+F L CI + E S CP+C
Sbjct: 18 QEEVICPICLD--ILQKP-VTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 178 EDVCPTCLDEYTPENPKITTRCSHHFHLGCIYEW---LERSESCPIC 221
E C CL EY E + C H+F CI W LER CP+C
Sbjct: 15 EASCSVCL-EYLKE--PVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEME 226
C H F CI +LE S+ CPIC ++
Sbjct: 34 CLHSFCKTCIVRYLETSKYCPICDVQVH 61
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEME 226
C H F CI +LE S+ CPIC ++
Sbjct: 30 CLHSFCKTCIVRYLETSKYCPICDVQVH 57
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 199 CSHHFHLGCIYEWLERSESCPICGKEME 226
C H F CI +LE S+ CPIC ++
Sbjct: 34 CLHSFCKTCIVRYLETSKYCPICDVQVH 61
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 28.5 bits (62), Expect = 3.7, Method: Composition-based stats.
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 207 CIYEWLERSESCPICGKE 224
C Y++ E ESCP CG E
Sbjct: 587 CGYQFTEDRESCPKCGSE 604
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 28.1 bits (61), Expect = 4.0, Method: Composition-based stats.
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 207 CIYEWLERSESCPICGKE 224
C Y++ E ESCP CG E
Sbjct: 587 CGYQFTEDRESCPKCGSE 604
>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 = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 181 CPTCL-DEYTPENPKITTRCSHHFHLGCIYEWLERSESCPIC 221
CP CL D +T C H H C E L+ CP+C
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
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
0.319 0.135 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,835,721
Number of Sequences: 62578
Number of extensions: 253722
Number of successful extensions: 567
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 524
Number of HSP's gapped (non-prelim): 49
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
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: 50 (23.9 bits)