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= 000906
(1231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2K2C|A Chain A, Solution Nmr Structure Of N-Terminal Domain Of Human Pirh2.
Northeast Structural Genomics Consortium (Nesg) Target
Ht2a
Length = 137
Score = 116 bits (290), Expect = 9e-26, Method: Composition-based stats.
Identities = 54/118 (45%), Positives = 69/118 (58%), Gaps = 5/118 (4%)
Query: 1006 GCKHYKRNCKLVATCCNSLYTCIRCHDEVADHALDRKSISEMMCMKCLIIQPVGSTCSTT 1065
GC+HY R C L A CC+ LYTC CHD DH LDR + E+ C+ C IQ TC
Sbjct: 19 GCEHYDRGCLLKAPCCDKLYTCRLCHDNNEDHQLDRFKVKEVQCINCEKIQHAQQTCEEC 78
Query: 1066 SCKNFSMARYYCRICKLFDDEREIYHCPYCNLCRVGKGLGIDYFHCMNCNACMSRSLQ 1123
S YYC IC LFD +++ YHC C +CR+G D+FHC+ CN C++ +LQ
Sbjct: 79 ST---LFGEYYCDICHLFDKDKKQYHCENCGICRIGPKE--DFFHCLKCNLCLAMNLQ 131
>pdb|2DKT|A Chain A, Solution Structure Of The Chy Zinc Finger Domain Of The Ring
Finger And Chy Zinc Finger Domain-Containing Protein 1
From Mus Musculus
Length = 143
Score = 103 bits (256), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 52/118 (44%), Positives = 68/118 (57%), Gaps = 5/118 (4%)
Query: 1006 GCKHYKRNCKLVATCCNSLYTCIRCHDEVADHALDRKSISEMMCMKCLIIQPVGSTCSTT 1065
GC+HY R C L A CC+ LYTC CHD DH LDR + E+ C+ C +Q TC
Sbjct: 18 GCEHYDRACLLKAPCCDKLYTCRLCHDTNEDHQLDRFKVKEVQCINCEKLQHAQQTCEDC 77
Query: 1066 SCKNFSMARYYCRICKLFDDEREIYHCPYCNLCRVGKGLGIDYFHCMNCNACMSRSLQ 1123
S YYC IC LFD ++ YHC C +CR+G D+FHC+ CN C++ +L+
Sbjct: 78 S---TLFGEYYCSICHLFDKDKRQYHCESCGICRIGPKE--DFFHCLKCNLCLTTNLR 130
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 52.4 bits (124), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 1129 EKSFMDNCPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKS 1180
E NCPIC ED+ +S A LPCGH++H TC+++ Y CP+C S
Sbjct: 1 ENVSQQNCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCMHS 52
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger And
Chy Zinc Finger Domain-Containing Protein 1 From Mus
Musculus
Length = 55
Score = 50.4 bits (119), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 1130 KSFMDNCPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICS 1178
S CPIC ED+ +S A LPCGH++H TC+++ Y CP+CS
Sbjct: 2 SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 48.5 bits (114), Expect = 3e-05, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 1136 CPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSL 1181
CP+C ED ++ + LPC H+ H +C + H +CP+C KSL
Sbjct: 18 CPVCKED-YALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 35.0 bits (79), Expect = 0.27, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 1136 CPICHEDLFSSTNPAKALP-CGHMMHSTCFQDYTCTHYTCPIC 1177
C +C +L A+ LP CGH H+ C + +H TCP+C
Sbjct: 8 CAVCLAEL-EDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.9 bits (76), Expect = 0.57, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 1133 MDNCPIC---HEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSL 1181
M +CPIC + ++ + + CGH+ S C +D TCP C K +
Sbjct: 3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 33.9 bits (76), Expect = 0.62, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 19/87 (21%)
Query: 1114 CNACMSRSLQ----VHICREK------------SFMDNCPIC---HEDLFSSTNPAKALP 1154
C+ C+ SL+ CR+K S +CPIC + ++ + +
Sbjct: 37 CSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTE 96
Query: 1155 CGHMMHSTCFQDYTCTHYTCPICSKSL 1181
CGH+ S C +D TCP C K +
Sbjct: 97 CGHVFCSQCLRDSLKNANTCPTCRKKI 123
Score = 33.5 bits (75), Expect = 0.84, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 17/83 (20%)
Query: 1135 NCPIC---HEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSLGDMKVYFSML 1191
+CPIC + ++ + + CGH+ S C +D TCP C K + + +
Sbjct: 9 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH---- 64
Query: 1192 DALLAEEKMPPEYLGQTQVRNPL 1214
P Y+G V P+
Sbjct: 65 ----------PIYIGSGTVSCPI 77
>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 = 33.5 bits (75), Expect = 0.74, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 1135 NCPIC---HEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSL 1181
+CPIC + ++ + + CGH+ S C +D TCP C K +
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38
Length = 75
Score = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 1136 CPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSLG 1182
C +C D F S + LPC H H+ C + + TCPIC G
Sbjct: 26 CVVCMCD-FESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSG 71
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 1135 NCPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPIC 1177
C IC + + LPC H+ H C + T+ CPIC
Sbjct: 16 KCTICL-SILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPIC 57
>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 = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 1130 KSFMDNCPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPIC 1177
+ + CPIC ED +N + ALPC H C + + TCP+C
Sbjct: 2 ATVAERCPICLED---PSNYSMALPCLHAFCYVCITRWIRQNPTCPLC 46
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 1136 CPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSLGDMKVYFSMLD 1192
C IC E A L C H S C ++ CPIC K + K Y +LD
Sbjct: 56 CIICSEYFI----EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS-KTYSLVLD 107
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 31.2 bits (69), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 1136 CPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSLGDMKVYFSMLD 1192
C IC E A L C H S C ++ CPIC K + K Y +LD
Sbjct: 56 CIICSEYFI----EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS-KTYSLVLD 107
>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 = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 1136 CPICHEDLFSSTNPAKALPCGHMMHSTCFQDYTCTHYTCPICSKSLGDMKVYFSMLD 1192
C IC E + L C H S C ++ CPIC K + K Y +LD
Sbjct: 67 CIICSEYFIEAV----TLNCAHSFCSYCINEWMKRKIECPICRKDIKS-KTYSLVLD 118
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.4 bits (67), Expect = 6.0, Method: Composition-based stats.
Identities = 30/118 (25%), Positives = 53/118 (44%), Gaps = 24/118 (20%)
Query: 546 AKKYETSCSSGTGLLISFPQTIRTFDPLPKLSVEKSCSGSIIDEPIPMDLIFF---FHKA 602
A+K CS G+ LL +FP+ + T +P+ +L E E +P L+ FHK
Sbjct: 150 ARKALDRCSEGSFLLTTFPRPV-TVEPMDQLDDE---------EGLPEKLVIKNQQFHKE 199
Query: 603 LKKDLDYLVFGSAQLAENALFLVEFHRRFNLIRLLYEIHSDAEDEIAFPAMEAKGKLQ 660
++ + A+ F E+ R+ + L E+ +D++ EA+ KL+
Sbjct: 200 REQ--------PPRFAQPGSFEYEYAMRW---KALIEMEKQQQDQVDRNIKEAREKLE 246
>pdb|2D9E|A Chain A, Solution Structure Of The Bromodomain Of Peregrin
pdb|2RS9|B Chain B, Solution Structure Of The Bromodomain Of Human Brpf1 In
Complex With Histone H4k5ac Peptide
Length = 121
Score = 30.0 bits (66), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 552 SCSSGTGLLISFPQTIRTFDPLPKLSVEKSCSGSIIDEPIPMDLIFFFHKALKKDLDYLV 611
S +G LI +T+ +++ +G+I EP+P+ + + +KK +D+
Sbjct: 1 GSSGSSGFLILLRKTLE--------QLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFT 52
Query: 612 FGSAQLAENALFLVEFHRRFNLI 634
A L +F FNLI
Sbjct: 53 MKQNLEAYRYLNFDDFEEDFNLI 75
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 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,957,628
Number of Sequences: 62578
Number of extensions: 1483003
Number of successful extensions: 3305
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 3279
Number of HSP's gapped (non-prelim): 37
length of query: 1231
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1121
effective length of database: 8,089,757
effective search space: 9068617597
effective search space used: 9068617597
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: 57 (26.6 bits)