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= 045854
(272 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTENVSIIHGY 80
CPICL S C H FCY CI W + + CPLCK S++H
Sbjct: 8 CPICLEDPSNYSMALPCLHAFCYVCITRWIR----------QNPTCPLCKVPVESVVHTI 57
Query: 81 DG 82
+
Sbjct: 58 ES 59
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVK-CPLCKTENVS 75
CPICL + +C H+FC +CI+ ++L S K CP C+ + VS
Sbjct: 57 CPICLDMLKNTMTTKECLHRFCADCII----------TALRSGNKECPTCRKKLVS 102
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 35.4 bits (80), Expect = 0.037, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKT 71
CPICL + + +D C H FC CI + KCPLCKT
Sbjct: 23 CPICLDILQKPVTID-CGHNFCLKCITQIGETSCG-------FFKCPLCKT 65
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 34.3 bits (77), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVK-CPLCKTENVS 75
CPICL + +C H+FC +CI+ ++L S K CP C+ + VS
Sbjct: 56 CPICLDMLKNTMTTKECLHRFCADCII----------TALRSGNKECPTCRKKLVS 101
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 33.9 bits (76), Expect = 0.087, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLC 69
C IC G +++ + + +C H FC +CIV +H S +CP C
Sbjct: 18 CSICKGYLIDATTITECLHTFCKSCIV--------RH--FYYSNRCPKC 56
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVK-CPLCKTENVS 75
CPICL + +C H+FC +CI+ ++L S K CP C+ + VS
Sbjct: 37 CPICLDMLKNTMTTKECLHRFCADCII----------TALRSGNKECPTCRKKLVS 82
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 33.1 bits (74), Expect = 0.15, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 21 CPICLGPVVEDSYLDK---CFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLC 69
CPIC+ E+ K C H C C+ K++AS ++ V+CP C
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCL---EKLLASS----INGVRCPFC 62
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 16 ENPNPCPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCK 70
EN C IC +E L+ C H FC CI W K ++CP+C+
Sbjct: 51 ENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMK----------RKIECPICR 94
>pdb|3H0L|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
Length = 478
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 17 NPNPCPICLG-----PVVEDSYLDKCFH-KFCYNCIVHWTKVVASKH 57
N N CP+CLG P+V ++ NC VH V A KH
Sbjct: 36 NTNVCPVCLGMPGALPIVNKRAVEYAIRASLALNCEVHEESVFARKH 82
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 11/57 (19%)
Query: 16 ENPNPCPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
EN C IC +E L+ C H FC CI W K ++CP+C+ +
Sbjct: 51 ENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMK----------RKIECPICRKD 96
>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 = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 11/57 (19%)
Query: 16 ENPNPCPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
EN C IC +E L+ C H FC CI W K ++CP+C+ +
Sbjct: 62 ENELQCIICSEYFIEAVTLN-CAHSFCSYCINEWMK----------RKIECPICRKD 107
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
C +C G ++ + + +C H FC CIV + L +S CP+C +
Sbjct: 18 CVLCGGYFIDATTIIECLHSFCKTCIVRY----------LETSKYCPICDVQ 59
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
C +C G ++ + + +C H FC CIV + L +S CP+C +
Sbjct: 18 CVLCGGYFIDATTIIECLHSFCKTCIVRY----------LETSKYCPICDVQ 59
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 31.6 bits (70), Expect = 0.54, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLC 69
CPICL + + +D C H FC CI + KCPLC
Sbjct: 23 CPICLDILQKPVTID-CGHNFCLKCITQIGETSC-------GFFKCPLC 63
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 11/57 (19%)
Query: 17 NPN-PCPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
NP+ C +C G ++ + + +C H FC CIV + L +S CP+C +
Sbjct: 9 NPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRY----------LETSKYCPICDVQ 55
>pdb|3HQ7|A Chain A, Ccpa From G. Sulfurreducens, G94kK97QR100I VARIANT
Length = 345
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 95 GDSFFFSKAHRYRLQSYYTEPGILNDVFNVSRYWKSR 131
GD S H+++ Q P +LN VFN +++W R
Sbjct: 84 GDLQATSTGHKWQ-QGPINAPTVLNSVFNTAQFWDGR 119
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 13/53 (24%)
Query: 21 CPICLGPVV---EDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCK 70
C +CL + E +L +C H F C+ W HS+ CPLC+
Sbjct: 8 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWL----GSHST------CPLCR 50
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 11/52 (21%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLCKTE 72
C ICL V L C H FCY C+ K +S L +C LC+ E
Sbjct: 18 CAICLQTCVHPVSL-PCKHVFCYLCV---------KGASWLGK-RCALCRQE 58
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIVHWTKVVASKHSSLLSSVKCPLC 69
C +CL +++ + +C H FC CI W + L CP+C
Sbjct: 18 CSVCL-EYLKEPVIIECGHNFCKACITRWWE-------DLERDFPCPVC 58
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 28.9 bits (63), Expect = 2.8, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 16 ENPNPCPICLGPVVEDSYLDKCFHKFCYNCIV 47
E+ CPICL + E + C H+FC CI+
Sbjct: 23 ESKYECPICLMALRE-AVQTPCGHRFCKACII 53
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 28.9 bits (63), Expect = 3.3, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 21 CPICLGPVVEDSYLDKCFHKFCYNCIV 47
CPICL + E + C H+FC CI+
Sbjct: 9 CPICLMALRE-AVQTPCGHRFCKACII 34
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
0.321 0.135 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,285,483
Number of Sequences: 62578
Number of extensions: 321399
Number of successful extensions: 728
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 713
Number of HSP's gapped (non-prelim): 33
length of query: 272
length of database: 14,973,337
effective HSP length: 97
effective length of query: 175
effective length of database: 8,903,271
effective search space: 1558072425
effective search space used: 1558072425
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)