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= 032386
(142 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 9 VCSVCHGNFNVPCQANCSHWFCGNCIMLVWDHG-STLQACRCPLCR 53
C +C P A+C+H FC CI L ++ +T CP+CR
Sbjct: 21 TCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCR 66
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRIT 57
C +C P C H FC C++ + + +CPLC+ IT
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKG--PSQCPLCKNDIT 69
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 29.6 bits (65), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRIT 57
C +C F NC+H FC CI W + CP+CR+ I
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCIN-EW----MKRKIECPICRKDIK 98
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 29.3 bits (64), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRIT 57
C +C F NC+H FC CI + + CP+CR+ I
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCI-----NEWMKRKIECPICRKDIK 98
>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 = 29.3 bits (64), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRIT 57
C +C F NC+H FC CI + + CP+CR+ I
Sbjct: 67 CIICSEYFIEAVTLNCAHSFCSYCI-----NEWMKRKIECPICRKDIK 109
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 28.9 bits (63), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 9 VCSVCHGNF-NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRITLLIPNDDSLR 67
+C +C N C H FC +CI+ G+ CP CR+++ + SLR
Sbjct: 36 MCPICLDMLKNTMTTKECLHRFCADCIITALRSGNK----ECPTCRKKLV----SKRSLR 87
Query: 68 QRHDPAVGDILQKV 81
DP ++ K+
Sbjct: 88 P--DPNFDALISKI 99
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 9 VCSVCHGNF-NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRITLLIPNDDSLR 67
+C +C N C H FC +CI+ G+ CP CR+++ + SLR
Sbjct: 55 MCPICLDMLKNTMTTKECLHRFCADCIITALRSGNK----ECPTCRKKLV----SKRSLR 106
Query: 68 QRHDPAVGDILQKV 81
DP ++ K+
Sbjct: 107 P--DPNFDALISKI 118
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 18 NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRI 56
N C H FC +CI+ G+ CP CR+++
Sbjct: 66 NTMTTKECLHRFCADCIITALRSGNK----ECPTCRKKL 100
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 9 VCSVCHGNFNVPCQANCSHWFCGNCIMLVWDHG 41
+CS C P QA C H +C C+ + G
Sbjct: 33 LCSACRNVLRRPFQAQCGHRYCSFCLASILSSG 65
>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e
Mutant From Human Bptf In The H3(1-9)k4me2 Bound State
Length = 174
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/111 (19%), Positives = 45/111 (40%), Gaps = 16/111 (14%)
Query: 14 HGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRR---ITLLIPNDDSLRQRH 70
F + C C +W+ G C+ ++ + CP C+ +T+L P L ++
Sbjct: 19 ESKFYIGCD-RCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTP----LTEKD 73
Query: 71 DPAVGDILQKVESYNRI--FGGPTTAN------GLFQRIQDLPFLLRRLVR 113
+ +L+ ++++ F P N G+ + DL + R+ R
Sbjct: 74 YEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQR 124
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 9 VCSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRI 56
+C +C P +C H FC CI + + +CPLC+ +
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFF--KCPLCKTSV 67
>pdb|3QZV|A Chain A, Crystal Structure Of Bptf Phd-Linker-Bromo In Complex With
Histone H4k12ac Peptide
Length = 174
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/111 (19%), Positives = 45/111 (40%), Gaps = 16/111 (14%)
Query: 14 HGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRR---ITLLIPNDDSLRQRH 70
F + C C +W+ G C+ ++ + CP C+ +T+L P L ++
Sbjct: 19 ESKFYIGCD-RCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTP----LTEKD 73
Query: 71 DPAVGDILQKVESYNRI--FGGPTTAN------GLFQRIQDLPFLLRRLVR 113
+ +L+ ++++ F P N G+ + DL + R+ R
Sbjct: 74 YEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQR 124
>pdb|3KV5|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV5|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With N-Oxalylglycine
pdb|3KV6|A Chain A, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
pdb|3KV6|D Chain D, Structure Of Kiaa1718, Human Jumonji Demethylase, In
Complex With Alpha-Ketoglutarate
Length = 488
Score = 27.3 bits (59), Expect = 3.3, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 17 FNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLC 52
F + C C WF G+C+ + H + CP C
Sbjct: 51 FMIECDI-CKDWFHGSCVGVEEHHAVDIDLYHCPNC 85
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRIT 57
C +C P C+H C C + S CP CRRR++
Sbjct: 18 CGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLC----CPFCRRRVS 61
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 26.2 bits (56), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 9 VCSVCHGNF-NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRITLLIPNDDSLR 67
+C +C G F + C H FC CI+ + CP+C ++ P L
Sbjct: 17 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK-----YCPICDVQVHKTRP---LLN 68
Query: 68 QRHDPAVGDILQKV 81
R D + DI+ K+
Sbjct: 69 IRSDKTLQDIVYKL 82
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 26.2 bits (56), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 9 VCSVCHGNF-NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRITLLIPNDDSLR 67
+C +C G F + C H FC CI+ + CP+C ++ P L
Sbjct: 13 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK-----YCPICDVQVHKTRP---LLN 64
Query: 68 QRHDPAVGDILQKV 81
R D + DI+ K+
Sbjct: 65 IRSDKTLQDIVYKL 78
>pdb|2ECY|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger)" Domain Of Tnf Receptor-Associated Factor 3
Length = 66
Score = 25.8 bits (55), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 10 CSVCHGNFNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRI 56
C CH P Q C H FC +C+ + S +C C+ I
Sbjct: 18 CEKCHLVLCSPKQTECGHRFCESCMAALLSSSSP----KCTACQESI 60
>pdb|3KV4|A Chain A, Structure Of Phf8 In Complex With Histone H3
Length = 447
Score = 25.8 bits (55), Expect = 7.9, Method: Composition-based stats.
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 17 FNVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLC 52
F + C C WF G+C+ + + + + CP C
Sbjct: 19 FMIECDM-CQDWFHGSCVGVEEEKAADIDLYHCPNC 53
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 25.8 bits (55), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 9 VCSVCHGNF-NVPCQANCSHWFCGNCIMLVWDHGSTLQACRCPLCRRRITLLIPNDDSLR 67
+C +C G F + C H FC CI+ + CP+C ++ P L
Sbjct: 17 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK-----YCPICDVQVHKTRP---LLN 68
Query: 68 QRHDPAVGDILQKV 81
R D + DI+ K+
Sbjct: 69 IRSDKTLQDIVYKL 82
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 0.146 0.499
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,462,966
Number of Sequences: 62578
Number of extensions: 162525
Number of successful extensions: 486
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 450
Number of HSP's gapped (non-prelim): 45
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
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: 46 (22.3 bits)