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= 002484
(917 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 859 TETESPTDLEPCC-ICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICKTTALP 916
TE E CC IC EY GD L C H FH C+ +WL + CP+C+ P
Sbjct: 31 TEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 50.4 bits (119), Expect = 5e-06, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 870 CCICQEEYTDGDDLGVLD-CGHNFHTDCIKLWLMQKNLCPICKTTAL 915
C +C E DG++ L CGH FH +C+ +WL + CP+C+ T +
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 49.3 bits (116), Expect = 9e-06, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 868 EPCCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICKTTAL 915
E C +C E++ D+LG+ C H FH C+ WL + +CP+C L
Sbjct: 16 ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 854 EKYVSTETESPTDLEPCCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICKTT 913
E++V + E P +C+E+Y G+ + L C H FH CI WL Q + CP+C+ +
Sbjct: 9 EEHVGSGLECP-------VCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKS 61
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 867 LEPCCICQEEYTDGDDLGVL-DCGHNFHTDCIKLWLMQKNLCPICK 911
++ C CQ E D + V +C H+FH C+ LW+ Q N CP+C+
Sbjct: 26 MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 45.1 bits (105), Expect = 2e-04, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
C IC +G+D+ L C H FH C+ WL+ CPIC+
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICR 58
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICKTTALPT 917
C +C ++ L VL C H FH C+ WL CPIC+ + P+
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS 73
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
C IC E + + L+C H+F + CI W+ +K CPIC+
Sbjct: 56 CIICSEYFIEAV---TLNCAHSFCSYCINEWMKRKIECPICR 94
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
C IC E + + L+C H+F + CI W+ +K CPIC+
Sbjct: 56 CIICSEYFIEAV---TLNCAHSFCSYCINEWMKRKIECPICR 94
>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 = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
C IC E + + L+C H+F + CI W+ +K CPIC+
Sbjct: 67 CIICSEYFIEAV---TLNCAHSFCSYCINEWMKRKIECPICR 105
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 37.7 bits (86), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 865 TDLEPCCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
TD E CCIC + D +L C H+F CI W + CPIC+
Sbjct: 13 TDEEECCICMDGRADL----ILPCAHSFCQKCIDKWSDRHRNCPICR 55
>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 = 34.3 bits (77), Expect = 0.32, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 864 PTDLEPCCICQEEYTDGDDLGVL----DCGHNFHTDCIKLWLMQKNLCPICK 911
P+ C IC + Y++ G L +CGH F + C++ L N CP C+
Sbjct: 7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 58
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 864 PTDLEPCCICQEEYTDGDDLGVL----DCGHNFHTDCIKLWLMQKNLCPICK 911
P+ C IC + Y++ G L +CGH F + C++ L N CP C+
Sbjct: 12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63
>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 = 33.9 bits (76), Expect = 0.42, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 866 DLEPCCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICKTT 913
DL C IC E + + + C HN+ + CI+ +L K CP C T
Sbjct: 21 DLLRCGICFEYFNIA--MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVT 66
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.9 bits (76), Expect = 0.43, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 870 CCICQEEYTDGDDLGVL----DCGHNFHTDCIKLWLMQKNLCPICK 911
C IC + Y++ G L +CGH F + C++ L N CP C+
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 51
>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 = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 868 EPCCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPICK 911
E C IC E+ ++ L C H F CI W+ Q CP+CK
Sbjct: 6 ERCPICLEDPSNYS--MALPCLHAFCYVCITRWIRQNPTCPLCK 47
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 865 TDLEP---CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPIC 910
T+L P C +C + D +++C H+F CI +L CPIC
Sbjct: 10 TELNPHLMCVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 865 TDLEP---CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPIC 910
T+L P C +C + D +++C H+F CI +L CPIC
Sbjct: 10 TELNPHLMCVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 865 TDLEP---CCICQEEYTDGDDLGVLDCGHNFHTDCIKLWLMQKNLCPIC 910
T+L P C +C + D +++C H+F CI +L CPIC
Sbjct: 6 TELNPHLMCVLCGGYFIDATT--IIECLHSFCKTCIVRYLETSKYCPIC 52
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 33.5 bits (75), Expect = 0.58, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 870 CCICQEEYTDGDDLGVL----DCGHNFHTDCIKLWLMQKNLCPICK 911
C IC + Y++ G L +CGH F + C++ L N CP C+
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 55
Score = 33.5 bits (75), Expect = 0.58, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 870 CCICQEEYTDGDDLGVL----DCGHNFHTDCIKLWLMQKNLCPICK 911
C IC + Y++ G L +CGH F + C++ L N CP C+
Sbjct: 75 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 120
>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 = 32.7 bits (73), Expect = 0.90, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL 78
>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 = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL 86
>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 = 1.2, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL 105
>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 = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL 96
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 67 CNHAFHFHCISRWLKTRQVCPL 88
>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 = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +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 = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 888 CGHNFHTDCIKLWLMQKNLCPI 909
C H FH CI WL + +CP+
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL 94
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 30.4 bits (67), Expect = 4.2, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 870 CCICQEEYTDGDDLGVLDCGHNFHTDCIKLW---LMQKNLCPIC 910
C +C E + +++CGHNF CI W L + CP+C
Sbjct: 18 CSVCLEYLKEPV---IIECGHNFCKACITRWWEDLERDFPCPVC 58
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
0.314 0.130 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,009,123
Number of Sequences: 62578
Number of extensions: 870932
Number of successful extensions: 1232
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1206
Number of HSP's gapped (non-prelim): 37
length of query: 917
length of database: 14,973,337
effective HSP length: 108
effective length of query: 809
effective length of database: 8,214,913
effective search space: 6645864617
effective search space used: 6645864617
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)