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= 011525
(484 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 = 1e-06, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 30/59 (50%)
Query: 221 CSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVH 279
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 = 1e-06, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 30/59 (50%)
Query: 221 CSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYVGDNYVH 279
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 = 5e-04, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 229 NLWVCL--ICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIWDYV 273
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 = 0.002, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 230 LWVCLICGFVGCGR-YKEGHAVRHW---KDTQHWYSLDLRTQQIWDYVGDNYV 278
+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 = 0.006, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 66/163 (40%), Gaps = 37/163 (22%)
Query: 221 CSVCGTVENLWVCLICGFVGCG-RYKEG-----HAVRHWKDTQHWYSLDLRT-----QQI 269
CS C ENLW+ L G + CG RY +G HAV H+++T + ++ L T +
Sbjct: 218 CSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADV 277
Query: 270 WDYVGDNYV--------------HRLNQSKADGKLVEMNSPCMSHEAHCGTCECSEDSGI 315
+ Y D+ V L K D + E+ + G E ++SG+
Sbjct: 278 YSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTDKTMTELE---IDMNQRIGEWELIQESGV 334
Query: 316 S-GALFNSKVEAIVDEYN--------RLLATQLETQRQYYESL 349
LF I + N ++L + + QR+Y + L
Sbjct: 335 PLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKL 377
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 36.2 bits (82), Expect = 0.044, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 221 CSVCGTVENLWVCLICGFVGCGRY------KEGHAVRHWKDTQHWYSLDLRT 266
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 = 0.059, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 221 CSVCGTVENLWVCLICGFVGCG-RYKEG-----HAVRHWKDTQHWYSLDLRT 266
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 = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 224 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 274 GD 275
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 = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 224 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 274 GD 275
G+
Sbjct: 109 GN 110
>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 = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 4/95 (4%)
Query: 196 SCTAKWTVLSCQVCRFCHQQDERPTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKD 255
+WTV + F ++ + P+ SV G + L+ ICG + ++ HA + ++
Sbjct: 33 GLVTEWTVQGQPILYFDRERFQDPSLSVRGGIPILFP--ICGNLPQDQFN--HAGKSYRL 88
Query: 256 TQHWYSLDLRTQQIWDYVGDNYVHRLNQSKADGKL 290
QH ++ DL + I DN L S D L
Sbjct: 89 KQHGFARDLPWEVIGQQTQDNARLDLRLSHNDATL 123
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 224 CGTVENL-----WVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
CGT + ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 46 CGTCHEINSGATFMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 103
Query: 274 GD 275
G+
Sbjct: 104 GN 105
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 170 CPICLERLDP-DTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCH 213
C +CLE P D GI C H+F C KW + +VC C+
Sbjct: 18 CAVCLEDFKPRDELGICP--CKHAFHRKCLIKWLEVR-KVCPLCN 59
>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 = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 169 TCPICLERLDPDTSGILSTICDHSFQCSCTA---KWTVL-----SCQVCRFCHQQDE-RP 219
TCPICLE L + LS C HSF +C K ++L SC VCR +Q + RP
Sbjct: 21 TCPICLELL----TQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRP 76
Query: 220 TCSVCGTVE 228
V VE
Sbjct: 77 NRHVANIVE 85
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 28.9 bits (63), Expect = 6.2, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 18/58 (31%)
Query: 170 CPICLERLDPDTSGILSTICDHSFQCSCTAKWTVLSCQVCRFCHQQ---DERPTCSVC 224
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 = 7.4, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 221 CSVCGTVENLWV----CLICGFVG-CGRYKEGHAVRHWKDTQH 258
C C + + WV C CG VG C HA RH+ T H
Sbjct: 21 CEECLKIGSPWVHLRICRTCGHVGCCDDSPHKHATRHFHATGH 63
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
0.319 0.132 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,521,384
Number of Sequences: 62578
Number of extensions: 528408
Number of successful extensions: 1240
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1229
Number of HSP's gapped (non-prelim): 30
length of query: 484
length of database: 14,973,337
effective HSP length: 103
effective length of query: 381
effective length of database: 8,527,803
effective search space: 3249092943
effective search space used: 3249092943
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)