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= 016340
(391 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
Length = 109
Score = 51.6 bits (122), Expect = 8e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 30/59 (50%)
Query: 128 CSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVH 186
C CGT++ WVCL C V CGRY GH ++H ++ H L W Y YVH
Sbjct: 27 CGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH 85
>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And
Ubiquitin C-Terminal Peptide Rlrgg
pdb|3PHD|A Chain A, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|B Chain B, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|C Chain C, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|D Chain D, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
Length = 107
Score = 51.6 bits (122), Expect = 8e-07, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 30/59 (50%)
Query: 128 CSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVH 186
C CGT++ WVCL C V CGRY GH ++H ++ H L W Y YVH
Sbjct: 25 CGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVH 83
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 136 NLWVCL--ICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYV 180
NLW CL C +VGCG + H+ H ++T+H+ +++L T ++W Y
Sbjct: 37 NLWACLENRCSYVGCGESQVDHSTIHSQETKHYLTVNLTTLRVWCYA 83
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain
Length = 126
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 137 LWVCLICGFVGCGR-YKEGHAVRHW---KDTQHWYSLDLRTQQIWDYVGDNYV 185
+W+CL CG GCGR +E HA++H+ + H L L +W YV DN V
Sbjct: 54 VWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEV 106
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 128 CSVCGTVENLWVCLICGFVGCG-RYKEG-----HAVRHWKDTQHWYSLDLRT 173
CS C ENLW+ L G + CG RY +G HAV H+++T + ++ L T
Sbjct: 218 CSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGT 269
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 128 CSVCGTVENLWVCLICGFVGCGRY------KEGHAVRHWKDTQHWYSLDLRT 173
C+ C ENLW+ L G V CG++ GHA+ H++D + ++ L T
Sbjct: 26 CARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGT 77
>pdb|2G43|A Chain A, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G43|B Chain B, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G45|A Chain A, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
pdb|2G45|D Chain D, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
Length = 129
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 128 CSVCGTVENLWVCLICGFVGCG-RYKEG-----HAVRHWKDTQHWYSLDLRT 173
CS C ENLW+ L G + CG RY +G HAV H+++T + ++ L T
Sbjct: 37 CSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGT 88
>pdb|3MHH|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE
pdb|3MHS|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND
Ubiquitin Aldehyde
pdb|4FJC|A Chain A, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
pdb|4FJC|E Chain E, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
Length = 476
Score = 31.6 bits (70), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 131 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 180
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 181 GD 182
G+
Sbjct: 109 GN 110
>pdb|4FIP|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FIP|E Chain E, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FK5|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11SUS1SGF73 DUB MODULE
Length = 476
Score = 31.6 bits (70), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 131 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 180
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 181 GD 182
G+
Sbjct: 109 GN 110
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 131 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 180
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 46 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 103
Query: 181 GD 182
G+
Sbjct: 104 GN 105
>pdb|3K25|A Chain A, Crystal Structure Of Slr1438 Protein From Synechocystis
Sp. Pcc 6803, Northeast Structural Genomics Consortium
Target Sgr112
pdb|3K25|B Chain B, Crystal Structure Of Slr1438 Protein From Synechocystis
Sp. Pcc 6803, Northeast Structural Genomics Consortium
Target Sgr112
Length = 289
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 4/95 (4%)
Query: 103 SCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKD 162
+WTV + F ++ + P+ SV G + L+ ICG + ++ HA + ++
Sbjct: 33 GLVTEWTVQGQPILYFDRERFQDPSLSVRGGIPILFP--ICGNLPQDQFN--HAGKSYRL 88
Query: 163 TQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKL 197
QH ++ DL + I DN L S D L
Sbjct: 89 KQHGFARDLPWEVIGQQTQDNARLDLRLSHNDATL 123
>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 = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 76 TCPICLERLDPDTSGILSTICDHSFQCSCTA---KWTVL-----SCQVCRFCHQQDE-RP 126
TCPICLE L + LS C HSF +C K ++L SC VCR +Q + RP
Sbjct: 21 TCPICLELL----TQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRP 76
Query: 127 TCSVCGTVE 135
V VE
Sbjct: 77 NRHVANIVE 85
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 77 CPICLERLDP-DTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCH 120
C +CLE P D GI C H+F C KW + +VC C+
Sbjct: 18 CAVCLEDFKPRDELGICP--CKHAFHRKCLIKWLEVR-KVCPLCN 59
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 18/58 (31%)
Query: 77 CPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQ---DERPTCSVC 131
CP+C+E L+ D F C+C Q+CRFC + DE C C
Sbjct: 3 CPLCMEPLEIDDINF--------FPCTC-------GYQICRFCWHRIRTDENGLCPAC 45
>pdb|2IDA|A Chain A, Solution Nmr Structure Of Protein Rpa1320 From
Rhodopseudomonas Palustris. Northeast Structural
Genomics Consortium Target Rpt3; Ontario Center For
Structural Proteomics Target Rp1313
Length = 102
Score = 28.9 bits (63), Expect = 5.7, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 128 CSVCGTVENLWV----CLICGFVG-CGRYKEGHAVRHWKDTQH 165
C C + + WV C CG VG C HA RH+ T H
Sbjct: 21 CEECLKIGSPWVHLRICRTCGHVGCCDDSPHKHATRHFHATGH 63
>pdb|1XM8|A Chain A, X-Ray Structure Of Glyoxalase Ii From Arabidopsis Thaliana
Gene At2g31350
pdb|1XM8|B Chain B, X-Ray Structure Of Glyoxalase Ii From Arabidopsis Thaliana
Gene At2g31350
pdb|2Q42|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Glyoxalase Ii From Arabidopsis Thaliana Gene At2g31350
pdb|2Q42|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Glyoxalase Ii From Arabidopsis Thaliana Gene At2g31350
Length = 254
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 226 LFNSKVEAIVDEYNRLLATQLETQRQYYESLLAEAKSKRESLIPETV--EKA----VASK 279
L NSK ++ N +L Q Y + +AE +SK+ IP TV EKA + S
Sbjct: 173 LSNSKFALSLEPNNEVL--------QSYAAHVAELRSKKLPTIPTTVKMEKACNPFLRSS 224
Query: 280 MQDIQNELDICEEAKKAVA 298
DI+ L I E A +A A
Sbjct: 225 NTDIRRALRIPEAADEAEA 243
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 0.130 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,681,296
Number of Sequences: 62578
Number of extensions: 410536
Number of successful extensions: 977
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 965
Number of HSP's gapped (non-prelim): 30
length of query: 391
length of database: 14,973,337
effective HSP length: 101
effective length of query: 290
effective length of database: 8,652,959
effective search space: 2509358110
effective search space used: 2509358110
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)