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= 032009
(149 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 = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 47/109 (43%), Positives = 59/109 (54%), Gaps = 4/109 (3%)
Query: 29 EPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYL 88
PL C HLVA A + PC C ENW+CL C +V C R++N HMLQH+
Sbjct: 2 SPLPWCPHLVAVCPIPAAGLDV-TQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHG 60
Query: 89 ETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137
+ H + LSY DLS WC+ C AY++ Q L V A+ KFGE P
Sbjct: 61 NSGHPLVLSYIDLSAWCYYCQAYVHHQA---LLDVKNIAHQNKFGEDMP 106
>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 = 85.1 bits (209), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 47/108 (43%), Positives = 59/108 (54%), Gaps = 4/108 (3%)
Query: 30 PLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLE 89
PL C HLVA A + PC C ENW+CL C +V C R++N HMLQH+
Sbjct: 1 PLPWCPHLVAVCPIPAAGLDV-TQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGN 59
Query: 90 TNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137
+ H + LSY DLS WC+ C AY++ Q L V A+ KFGE P
Sbjct: 60 SGHPLVLSYIDLSAWCYYCQAYVHHQA---LLDVKNIAHQNKFGEDMP 104
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain
Length = 126
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 65 WLCLCCKEVLCSRFVN-KHMLQHYLETN---HSVALSYSDLSVWCFTCD 109
WLCL C C R +H L+HYL H + LS + SVWC+ CD
Sbjct: 55 WLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCD 103
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 46 AHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFV------NKHMLQHYLETNHSVALSYS 99
A IP C++C WL L +LC R N H ++HY ET + +A+
Sbjct: 209 ARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLG 268
Query: 100 DLS 102
++
Sbjct: 269 TIT 271
>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 = 33.9 bits (76), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 46 AHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFV------NKHMLQHYLETNHSVALSYS 99
A IP C++C WL L +LC R N H ++HY ET + +A+
Sbjct: 28 ARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLG 87
Query: 100 DLS 102
++
Sbjct: 88 TIT 90
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 33.1 bits (74), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 14/87 (16%)
Query: 22 GAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFV-- 79
G+ S + LT D+ V IP C RC WL L VLC ++
Sbjct: 1 GSVSKYANNLTQLDNGV--------RIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFD 52
Query: 80 ----NKHMLQHYLETNHSVALSYSDLS 102
N H L+HY + + +A+ ++
Sbjct: 53 SSGGNGHALEHYRDMGYPLAVKLGTIT 79
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 55 CNRCQHPSEN-WLCL--CCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTC--D 109
C C+ N W CL C V C H H ET H + ++ + L VWC+ C +
Sbjct: 28 CQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHSQETKHYLTVNLTTLRVWCYACSKE 87
Query: 110 AYLNAQVIPQ 119
+L+ ++ Q
Sbjct: 88 VFLDRKLGTQ 97
>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 = 29.6 bits (65), Expect = 0.70, Method: Composition-based stats.
Identities = 12/58 (20%), Positives = 26/58 (44%)
Query: 55 CNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYL 112
C C + +C + C + + H L H + H ++ ++ ++CF C+ Y+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
>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 = 29.6 bits (65), Expect = 0.73, Method: Composition-based stats.
Identities = 12/58 (20%), Positives = 26/58 (44%)
Query: 55 CNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYL 112
C C + +C + C + + H L H + H ++ ++ ++CF C+ Y+
Sbjct: 51 CGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 26/59 (44%)
Query: 54 PCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYL 112
C C + +C + C + + H L H + H ++ ++ ++CF C+ Y+
Sbjct: 45 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 103
>pdb|2G77|B Chain B, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 198
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 77 RFVNKHMLQHYLETNHSVAL--------SYSDLSVWCFTCDAYLNAQVIPQL 120
RF K M+QHY H+V S+ L W C +L A IP++
Sbjct: 90 RF-RKSMVQHYYRNVHAVVFVYDXTNXASFHSLPAWIEECKQHLLANDIPRI 140
>pdb|1Z06|A Chain A, Gppnhp-Bound Rab33 Gtpase
Length = 189
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 77 RFVNKHMLQHYLETNHSVAL--------SYSDLSVWCFTCDAYLNAQVIPQL 120
RF K M+QHY H+V S+ L W C +L A IP++
Sbjct: 81 RF-RKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRI 131
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 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,676,838
Number of Sequences: 62578
Number of extensions: 179509
Number of successful extensions: 374
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 364
Number of HSP's gapped (non-prelim): 14
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
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: 47 (22.7 bits)