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= 030350
(179 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 = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCR 142
CAVCL +E+ + R L C H FH EC+D W+ H TCPLCR
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS--HSTCPLCR 50
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQSKS 153
C +CL+ +EE + VR L C H+FH+ C+D+W+ + K CP+CR + L S+S
Sbjct: 17 CTICLSILEEGEDVRRL-PCMHLFHQVCVDQWLITN--KKCPICRVDIEAQLPSES 69
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 82 ASFGDIKVRMPWVPDTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLC 141
+S KV+ + + CAVCL + D + + C H FHR+C+ +W++ K CPLC
Sbjct: 2 SSGSSGKVKELNLHELCAVCLEDFKPRDELG-ICPCKHAFHRKCLIKWLEV--RKVCPLC 58
Query: 142 RAPLLTYLQ 150
P+L Q
Sbjct: 59 NMPVLQLAQ 67
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCRA 143
C VC+ E L+R L C H FH +C+D+W+ + +TCP+CRA
Sbjct: 26 CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN--RTCPICRA 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 = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 75 IKERLVLASFGDIKVRMPWVPDTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDH 134
+ E LV G + M C +C + + D+ EL C H FH+ C+ W+
Sbjct: 25 LPEILVTEDHGAVGQEM-----CCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKS- 77
Query: 135 HKTCPLCR 142
TCP+CR
Sbjct: 78 -GTCPVCR 84
>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 = 0.021, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCRAP 144
C +CL + +V + C H+ HR C + + + CPLC P
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYR--CPLCSGP 52
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 35.0 bits (79), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCRAPL 145
C VC + VR+L C H+FH CI W+ + H +CP+CR L
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWL--EQHDSCPVCRKSL 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 = 0.035, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 117 CCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQSKS 153
C H F ++CID+W D H+ CP+CR + +S
Sbjct: 32 CAHSFCQKCIDKW--SDRHRNCPICRLQMTGANESSG 66
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 33.5 bits (75), Expect = 0.060, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 94 VPDTCAVCLNHMEEDDLVRELRNCCHVFHRECIDR-WVDYDHHKTCPLC 141
V +C+VCL +++E ++ C H F + CI R W D + CP+C
Sbjct: 14 VEASCSVCLEYLKEPVIIE----CGHNFCKACITRWWEDLERDFPCPVC 58
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 91 MPWVPDTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQ 150
M V + C +CL E+ C H F CI RW+ + TCPLC+ P+ + +
Sbjct: 1 MATVAERCPICL---EDPSNYSMALPCLHAFCYVCITRWI--RQNPTCPLCKVPVESVVH 55
Query: 151 S 151
+
Sbjct: 56 T 56
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 94 VPDTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCR 142
V D C C +++D V C H FH C+ WV ++ CPLC+
Sbjct: 25 VMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNR--CPLCQ 71
>pdb|1KVP|A Chain A, Structural Analysis Of The Spiroplasma Virus, Spv4,
Implications For Evolutionary Variation To Obtain Host
Diversity Among The Microviridae, Electron Microscopy,
Alpha Carbons Only
Length = 497
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 90 RMPWVPDTCAVCLNHMEEDDLVRELRNCCHV 120
+ PW+PD N + +DD R CCH+
Sbjct: 136 KAPWMPDRTEANPNELNQDDARYGFR-CCHL 165
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKT-CPLC 141
C +C+ E+ L +L +C H R+C+++ + + CP C
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFC 62
>pdb|2BPA|1 Chain 1, Atomic Structure Of Single-Stranded Dna Bacteriophage
Phix174 And Its Functional Implications
pdb|1AL0|F Chain F, Procapsid Of Bacteriophage Phix174
Length = 426
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 90 RMPWVPDTCAVCLNHMEEDDLVRELRNCCHV 120
+ PW+PD N + +DD R CCH+
Sbjct: 136 KAPWMPDRTEANPNELNQDDARYGFR-CCHL 165
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHM--------------EEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ ++ C H FH CI RW+ + CP
Sbjct: 47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 104
Query: 140 L 140
L
Sbjct: 105 L 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 = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHMEE--------------DDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ + ++ C H FH CI RW+ + CP
Sbjct: 36 VVDNCAICRNHIXDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 93
Query: 140 L 140
L
Sbjct: 94 L 94
>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 = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHM--------------EEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ ++ C H FH CI RW+ + CP
Sbjct: 38 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 95
Query: 140 L 140
L
Sbjct: 96 L 96
>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 = 2.2, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHM--------------EEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ ++ C H FH CI RW+ + CP
Sbjct: 28 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 85
Query: 140 L 140
L
Sbjct: 86 L 86
>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 = 2.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHM--------------EEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ ++ C H FH CI RW+ + CP
Sbjct: 36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 93
Query: 140 L 140
L
Sbjct: 94 L 94
>pdb|1CD3|F Chain F, Procapsid Of Bacteriophage Phix174
Length = 426
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 90 RMPWVPDTCAVCLNHMEEDDLVRELRNCCHV 120
+ PW+PD N + +DD R CCH+
Sbjct: 136 KAPWMPDRTEANPNELNQDDARFGFR-CCHL 165
>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 = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 16/61 (26%)
Query: 94 VPDTCAVCLNHM--------------EEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCP 139
V D CA+C NH+ ++ C H FH CI RW+ + CP
Sbjct: 20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQVCP 77
Query: 140 L 140
L
Sbjct: 78 L 78
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 26/63 (41%), Gaps = 20/63 (31%)
Query: 94 VPDTCAVCLNHMEEDDLVRELRN----------------CCHVFHRECIDRWVDYDHHKT 137
V D CA+C NH+ DL E + C H FH CI RW+ +
Sbjct: 30 VVDNCAICRNHIM--DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--RQV 85
Query: 138 CPL 140
CPL
Sbjct: 86 CPL 88
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 116 NCCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQSKSLNN 156
NC H F CI+ W+ CP+CR + + S L+N
Sbjct: 70 NCAHSFCSYCINEWMKRKIE--CPICRKDIKSKTYSLVLDN 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 = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 116 NCCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQSKSLNN 156
NC H F CI+ W+ CP+CR + + S L+N
Sbjct: 81 NCAHSFCSYCINEWMKRKIE--CPICRKDIKSKTYSLVLDN 119
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 116 NCCHVFHRECIDRWVDYDHHKTCPLCRAPLLTYLQSKSLNN 156
NC H F CI+ W+ CP+CR + + S L+N
Sbjct: 70 NCAHSFCSYCINEWMKRKIE--CPICRKDIKSKTYSLVLDN 108
>pdb|2D8S|A Chain A, Solution Structure Of The Ring Domain Of The Human
Cellular Modulator Of Immune Recognition Protein
Length = 80
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 92 PWVPDTCAVCLNHMEEDDLVRELRNC-C----HVFHRECIDRWVDYDHHKTCPLCR 142
P D C +C H E DD + C C H H+ C+ +W+ + C LC+
Sbjct: 12 PSSQDICRIC--HCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCK 65
>pdb|1YO8|A Chain A, Structure Of The C-Terminal Domain Of Human
Thrombospondin-2
Length = 634
Score = 26.6 bits (57), Expect = 7.8, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 96 DTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVD--YDHHKTCPLCRAP 144
D C+V ++ DD+ E NC +V++ + D D DH CPL P
Sbjct: 250 DACSV---DIDGDDVFNERDNCPYVYNTDQRDTDGDGVGDHCDNCPLVHNP 297
>pdb|3VGO|A Chain A, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
pdb|3VGO|B Chain B, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
pdb|3VGO|C Chain C, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
Length = 394
Score = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 98 CAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVDYDHHKTCPLCR 142
C +C E+D ++ C H+ C+ W + D + CP CR
Sbjct: 341 CKIC----AENDKDVKIEPCGHLMCTSCLTAWQESD-GQGCPFCR 380
>pdb|2RHP|A Chain A, The Thrombospondin-1 Polymorphism Asn700ser Associated
With Cornoary Artery Disease Causes Local And
Long-Ranging Changes In Protein Structure
Length = 622
Score = 26.6 bits (57), Expect = 8.1, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 96 DTCAVCLNHMEEDDLVRELRNCCHVFHRECIDRWVD--YDHHKTCPLCRAP 144
D C+V ++ DD+ E NC +V++ + D D DH CPL P
Sbjct: 247 DACSV---DIDGDDVFNERDNCPYVYNTDQRDTDGDGVGDHCDNCPLVHNP 294
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
0.331 0.143 0.495
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,668,894
Number of Sequences: 62578
Number of extensions: 154088
Number of successful extensions: 438
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 412
Number of HSP's gapped (non-prelim): 33
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 bits)