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= 039031
(452 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
+ C ICL+++ + + +C H+F DCI +A S G +CP CRK
Sbjct: 55 LMCPICLDMLKN----TMTTKECLHRFCADCIITALRS-GNKECPTCRK 98
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 35 CSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
C ICL+++ + + +C H+F DCI +A S G +CP CRK
Sbjct: 37 CPICLDMLKN----TMTTKECLHRFCADCIITALRS-GNKECPTCRK 78
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 36.2 bits (82), Expect = 0.037, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 35 CSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
C ICL+++ + + +C H+F DCI +A S G +CP CRK
Sbjct: 56 CPICLDMLKN----TMTTKECLHRFCADCIITALRS-GNKECPTCRK 97
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 35.8 bits (81), Expect = 0.050, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGS----AFNSKGAMQCPNCR 80
V+C ICLEL+T L CGH F C+ + + KG CP CR
Sbjct: 20 VTCPICLELLTQP-----LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCR 66
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 35.8 bits (81), Expect = 0.052, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCR 80
V C++CL + D G+ + +CGH FH +C+ S CP CR
Sbjct: 6 VECAVCLAELED-GEEARFLPRCGHGFHAECVDMWLGSHST--CPLCR 50
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 35.8 bits (81), Expect = 0.053, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 32 TVSCSICLE---LVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
TVSC IC++ + NG R +CGH F C+ + K A CP CRK
Sbjct: 7 TVSCPICMDGYSEIVQNG-RLIVSTECGHVFCSQCLRDSL--KNANTCPTCRK 56
Score = 35.8 bits (81), Expect = 0.053, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 32 TVSCSICLE---LVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
TVSC IC++ + NG R +CGH F C+ + K A CP CRK
Sbjct: 72 TVSCPICMDGYSEIVQNG-RLIVSTECGHVFCSQCLRDSL--KNANTCPTCRK 121
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 35.8 bits (81), Expect = 0.055, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 32 TVSCSICLE---LVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
TVSC IC++ + NG R +CGH F C+ + K A CP CRK
Sbjct: 15 TVSCPICMDGYSEIVQNG-RLIVSTECGHVFCSQCLRDSL--KNANTCPTCRK 64
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 33 VSCSICLE---LVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
VSC IC++ + NG R +CGH F C+ + K A CP CRK
Sbjct: 4 VSCPICMDGYSEIVQNG-RLIVSTECGHVFCSQCLRDSL--KNANTCPTCRK 52
>pdb|1V87|A Chain A, Solution Structure Of The Ring-H2 Finger Domain Of Mouse
Deltex Protein 2
Length = 114
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 54 QCGHQFHLDCIGSAF---NSKGAMQCPNCRKI 82
+C H FHL C+ + + N G++QCP+C+ I
Sbjct: 60 KCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTI 91
>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 = 0.15, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 32 TVSCSICLE---LVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCRK 81
TVSC IC++ + NG R +CGH F C+ + K A CP CRK
Sbjct: 10 TVSCPICMDGYSEIVQNG-RLIVSTECGHVFCSQCLRDSL--KNANTCPTCRK 59
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIG----SAFNSKGAMQCPNCR 80
V+C ICLEL+ + C H F CI S N+ G CP CR
Sbjct: 20 VTCPICLELLKEP-----VSADCNHSFCRACITLNYESNRNTDGKGNCPVCR 66
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 32.3 bits (72), Expect = 0.60, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGS-AFNSKGAMQCPNCR 80
V C ICL+++ + + CGH F L CI S G +CP C+
Sbjct: 21 VICPICLDIL-----QKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCK 64
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 33 VSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGS-AFNSKGAMQCPNC 79
V C ICL+++ + + CGH F L CI S G +CP C
Sbjct: 21 VICPICLDIL-----QKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|3NW0|A Chain A, Crystal Structure Of Mageg1 And Nse1 Complex
Length = 238
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 55 CGHQFHLDCIGSAFNSKGAMQCPNC 79
CG + HL C+ F S +CP+C
Sbjct: 199 CGIRMHLPCVAKYFQSNAEPRCPHC 223
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 31 RTVSCSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNCR 80
+++SC IC ++ D + S C H F CI G+ CP+CR
Sbjct: 22 KSISCQICEHILADPVETS-----CKHLFCRICILRCLKVMGSY-CPSCR 65
>pdb|2CT0|A Chain A, Solution Structure Of The Ring Domain Of The Non-Smc
Element 1 Protein
Length = 74
Score = 28.1 bits (61), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 35 CSICLELVTDNGDRSWAKLQCGHQFHLDCIGSAFNSKGAMQCPNC 79
C+IC L+ + + CG + HL C+ F S +CP+C
Sbjct: 18 CNICHSLLI----QGQSCETCGIRMHLPCVAKYFQSNAEPRCPHC 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
0.316 0.131 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,657,778
Number of Sequences: 62578
Number of extensions: 556915
Number of successful extensions: 1094
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1086
Number of HSP's gapped (non-prelim): 22
length of query: 452
length of database: 14,973,337
effective HSP length: 102
effective length of query: 350
effective length of database: 8,590,381
effective search space: 3006633350
effective search space used: 3006633350
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)