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= 018432
(356 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 = 49.7 bits (117), Expect = 3e-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 = 49.3 bits (116), Expect = 3e-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 = 4e-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 = 40.0 bits (92), 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 = 0.005, Method: Compositional matrix adjust.
Identities = 42/159 (26%), Positives = 64/159 (40%), Gaps = 32/159 (20%)
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-GALFNSKVEAIVDEYNRLLATQLETQRQVSTSFPDVK 353
LF I + N + L + QV S PD +
Sbjct: 335 PLKPLFGPGYTGIRNLGN---SCYLNSVVQVLFSIPDFQ 370
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 35.8 bits (81), Expect = 0.040, 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 = 0.041, 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|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 = 32.0 bits (71), Expect = 0.50, 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|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 = 1.4, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 35/69 (50%), Gaps = 13/69 (18%)
Query: 169 TCPICLERLDPDTSGILSTICDHSFQCSCTA---KWTVL-----SCQVCRFCHQ-QDERP 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|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 = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 30/122 (24%)
Query: 167 LPTCPICLERLDPDTS--GILST------ICDHSFQCSCTAKWTVLSCQVCRFCHQQDER 218
+ CP + + S G+L T I +HS K L+ C CH+ +
Sbjct: 6 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHS-----VPKEKFLNTMKCGTCHEINSG 60
Query: 219 PTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
T ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 61 AT----------FMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 274 GD 275
G+
Sbjct: 109 GN 110
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 30/122 (24%)
Query: 167 LPTCPICLERLDPDTS--GILST------ICDHSFQCSCTAKWTVLSCQVCRFCHQQDER 218
+ CP + + S G+L T I +HS K L+ C CH+ +
Sbjct: 6 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHS-----VPKEKFLNTMKCGTCHEINSG 60
Query: 219 PTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
T ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 61 AT----------FMCLQCGFCGC--WNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Query: 274 GD 275
G+
Sbjct: 109 GN 110
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 30/122 (24%)
Query: 167 LPTCPICLERLDPDTS--GILST------ICDHSFQCSCTAKWTVLSCQVCRFCHQQDER 218
+ CP + + S G+L T I +HS K L+ C CH+ +
Sbjct: 1 MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHS-----VPKEKFLNTMKCGTCHEINSG 55
Query: 219 PTCSVCGTVENLWVCLICGFVGCGRYKEGHAVRHWKDTQHWYSLDLRTQQIW-----DYV 273
T ++CL CGF GC + H + H K H + ++ ++ DY+
Sbjct: 56 AT----------FMCLQCGFCGC--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 = 29.6 bits (65), Expect = 2.8, 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|1EPW|A Chain A, Crystal Structure Of Clostridium Neurotoxin Type B
pdb|1F31|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With A Trisaccharide
pdb|1I1E|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With Doxorubicin
pdb|1G9A|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 3)
pdb|1G9B|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 1)
pdb|1G9C|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 4)
pdb|1G9D|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 2)
pdb|1S0B|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 4.0
pdb|1S0C|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.0
pdb|1S0D|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.5
pdb|1S0E|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 6.0
pdb|1S0F|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 7.0
pdb|1S0G|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B Apo Form
pdb|2NP0|A Chain A, Crystal Structure Of The Botulinum Neurotoxin Type B
Complexed With Synaptotagamin-Ii Ectodomain
Length = 1290
Score = 28.9 bits (63), Expect = 5.1, Method: Composition-based stats.
Identities = 30/128 (23%), Positives = 52/128 (40%), Gaps = 12/128 (9%)
Query: 25 VSSTATRSRANPNPKFSERRGLVHLFRGTSQSYQQNPNSRSTCIFVVAVPNYLSSDEFVR 84
V TRS+ N N K+ R L+ G ++ NS+S +V +Y+ D F
Sbjct: 1117 VGEILTRSKYNQNSKYINYR---DLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFF-- 1171
Query: 85 FCGSHIDHVEELIFIRNDAMEDRYSVLIKLVDQLTADEFYSNLNGKRFSPAEAEVCHMLF 144
+++ + + E+ L + D +DEFY+ + K + C +LF
Sbjct: 1172 ----NLNQEWRVYTYKYFKKEEEKLFLAPISD---SDEFYNTIQIKEYDEQPTYSCQLLF 1224
Query: 145 MLSVEYTE 152
E T+
Sbjct: 1225 KKDEESTD 1232
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
0.322 0.134 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,890,788
Number of Sequences: 62578
Number of extensions: 438164
Number of successful extensions: 967
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 958
Number of HSP's gapped (non-prelim): 28
length of query: 356
length of database: 14,973,337
effective HSP length: 100
effective length of query: 256
effective length of database: 8,715,537
effective search space: 2231177472
effective search space used: 2231177472
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: 52 (24.6 bits)