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= 018247
(359 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 = 78.6 bits (192), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 33/55 (60%), Positives = 40/55 (72%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRRSLRDDLNYDALIAALYPDIDKY 56
ECLHRFC +CI A+R GN ECP CR S+RSLR D N+DALI+ +YP D+Y
Sbjct: 72 ECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEY 126
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 74.7 bits (182), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 31/50 (62%), Positives = 37/50 (74%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRRSLRDDLNYDALIAALYP 51
ECLHRFC +CI A+R GN ECP CR S+RSLR D N+DALI+ +YP
Sbjct: 71 ECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYP 120
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/49 (61%), Positives = 36/49 (73%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRRSLRDDLNYDALIAALY 50
ECLHRFC +CI A+R GN ECP CR S+RSLR D N+DALI+ +Y
Sbjct: 52 ECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIY 100
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 35.0 bits (79), Expect = 0.058, Method: Composition-based stats.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 3 CLHRFCRECIDKAMRLGNNECPACRTHC 30
C H FCR CI + +++ + CP+CR C
Sbjct: 41 CKHLFCRICILRCLKVMGSYCPSCRYPC 68
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 3 CLHRFCRECIDKAMRLGNNECPACRTHCASRRSLRDDLNYDALIAALYP 51
C H C++C+D++ R CPACR +++ + ++ L+P
Sbjct: 70 CQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVLNQLFP 118
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASRRSL---RDDLNYDALIAALYPDIDK 55
+ECLH FC+ CI + + + CP C R L R D ++ L P + K
Sbjct: 28 IECLHSFCKTCIVRYLET-SKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFK 84
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASRRSL---RDDLNYDALIAALYPDIDK 55
+ECLH FC+ CI + + + CP C R L R D ++ L P + K
Sbjct: 32 IECLHSFCKTCIVRYLET-SKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFK 88
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASRRSL---RDDLNYDALIAALYPDIDK 55
+ECLH FC+ CI + + + CP C R L R D ++ L P + K
Sbjct: 32 IECLHSFCKTCIVRYLET-SKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFK 88
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 3 CLHRFCRECIDKAMRLGNNECP 24
C HRFC+ CI K++R ++CP
Sbjct: 24 CGHRFCKACIIKSIRDAGHKCP 45
>pdb|1Z6U|A Chain A, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
pdb|1Z6U|B Chain B, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
Length = 150
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 23/54 (42%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRRSLRDDLNYDALIAALYPDIDK 55
EC H C++C+ ++ + CPACR + + L+ +P K
Sbjct: 95 ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPNEILQTLLDLFFPGYSK 148
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 32.7 bits (73), Expect = 0.36, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 3 CLHRFCRECIDKAMRLGNNECP 24
C HRFC+ CI K++R ++CP
Sbjct: 43 CGHRFCKACIIKSIRDAGHKCP 64
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
P1 Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The
C2 Space Group
Length = 118
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 3 CLHRFCRECIDKAMRLGNNECP 24
C HRFC+ CI K++R ++CP
Sbjct: 36 CGHRFCKACIIKSIRDAGHKCP 57
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 32.0 bits (71), Expect = 0.51, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPAC 26
ECLH FC+ CI + +N CP C
Sbjct: 33 ECLHTFCKSCIVRHFYY-SNRCPKC 56
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 31.6 bits (70), Expect = 0.66, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRR 34
EC H FC +C+ +++ N CP CR +R
Sbjct: 27 ECGHVFCSQCLRDSLK-NANTCPTCRKKINHKR 58
>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 = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACRTHCASRR 34
EC H FC +C+ +++ N CP CR +R
Sbjct: 34 ECGHVFCSQCLRDSLK-NANTCPTCRKKINHKR 65
>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 = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACR 27
+ CLH FC CI + +R N CP C+
Sbjct: 22 LPCLHAFCYVCITRWIR-QNPTCPLCK 47
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASR 33
+ C H FC CI++ M+ ECP CR S+
Sbjct: 69 LNCAHSFCSYCINEWMK-RKIECPICRKDIKSK 100
>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 = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASR 33
+ C H FC CI++ M+ ECP CR S+
Sbjct: 80 LNCAHSFCSYCINEWMK-RKIECPICRKDIKSK 111
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 3 CLHRFCRECIDKAMRLGNNECPA 25
C HRFC+ CI K++R ++CP
Sbjct: 36 CGHRFCKACIIKSIRDAGHKCPV 58
>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 = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 2 ECLHRFCRECIDKAMRLGNNECPACR 27
EC HRFC C+ + + +C AC+
Sbjct: 32 ECGHRFCESCMAALLSSSSPKCTACQ 57
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MECLHRFCRECIDKAMRLGNNECPACRTHCASR 33
+ C H FC CI++ M+ ECP CR S+
Sbjct: 69 LNCAHSFCSYCINEWMK-RKIECPICRKDIKSK 100
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
0.317 0.132 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,361,355
Number of Sequences: 62578
Number of extensions: 338204
Number of successful extensions: 642
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 30
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)