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= 023654
(279 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 = 84.7 bits (208), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 44/107 (41%), Positives = 61/107 (57%), Gaps = 4/107 (3%)
Query: 164 LTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQET 223
L C HLVA A + + PC C + NW+CL C +V C RY+N HMLQH+ +
Sbjct: 4 LPWCPHLVAVCPIPAAGL-DVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNS 62
Query: 224 NHSVALGYSDLSVWCFACHAYLNAQAILQLQPVHETAYVLKFGRALP 270
H + L Y DLS WC+ C AY++ QA+L ++ A+ KFG +P
Sbjct: 63 GHPLVLSYIDLSAWCYYCQAYVHHQALLDVK---NIAHQNKFGEDMP 106
Score = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 4/107 (3%)
Query: 31 LASCDHLVASLSSDLARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREK 90
L C HLVA A + PC C + NW+CL C +V C RY+N HML+H+
Sbjct: 4 LPWCPHLVAVCPIPAAGLDV-TQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNS 62
Query: 91 NHSVALDYSDLSVWCFACHAYLNAQAILQLRPVHETSYVLKFGRALP 137
H + L Y DLS WC+ C AY++ QA+L ++ + + KFG +P
Sbjct: 63 GHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQN---KFGEDMP 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 = 84.7 bits (208), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 44/107 (41%), Positives = 61/107 (57%), Gaps = 4/107 (3%)
Query: 164 LTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQET 223
L C HLVA A + + PC C + NW+CL C +V C RY+N HMLQH+ +
Sbjct: 2 LPWCPHLVAVCPIPAAGL-DVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNS 60
Query: 224 NHSVALGYSDLSVWCFACHAYLNAQAILQLQPVHETAYVLKFGRALP 270
H + L Y DLS WC+ C AY++ QA+L ++ A+ KFG +P
Sbjct: 61 GHPLVLSYIDLSAWCYYCQAYVHHQALLDVK---NIAHQNKFGEDMP 104
Score = 82.0 bits (201), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 4/107 (3%)
Query: 31 LASCDHLVASLSSDLARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREK 90
L C HLVA A + PC C + NW+CL C +V C RY+N HML+H+
Sbjct: 2 LPWCPHLVAVCPIPAAGLDV-TQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNS 60
Query: 91 NHSVALDYSDLSVWCFACHAYLNAQAILQLRPVHETSYVLKFGRALP 137
H + L Y DLS WC+ C AY++ QA+L ++ + + KFG +P
Sbjct: 61 GHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQN---KFGEDMP 104
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 156 AESGSVRHLTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYV--- 212
A G VR ++ + L ARIP C++C WL L +LC R
Sbjct: 187 AWDGEVRQVSKHAFSLKQLDNP-ARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDG 245
Query: 213 ---NKHMLQHYQETNHSVAL 229
N H ++HY+ET + +A+
Sbjct: 246 SGGNNHAVEHYRETGYPLAV 265
Score = 35.4 bits (80), Expect = 0.032, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 46 ARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYV------NKHMLRHYREKNHSVAL 96
ARIP C+ C WL L +LC R N H + HYRE + +A+
Sbjct: 209 ARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAV 265
>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 = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 7/102 (6%)
Query: 156 AESGSVRHLTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYV--- 212
A G VR ++ + L + ARIP C++C WL L +LC R
Sbjct: 6 AWDGEVRQVSKHAFSLKQLD-NPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDG 64
Query: 213 ---NKHMLQHYQETNHSVALGYSDLSVWCFACHAYLNAQAIL 251
N H ++HY+ET + +A+ ++ ++Y +L
Sbjct: 65 SGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVL 106
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 46 ARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYV------NKHMLRHYREKNHSVALDYS 99
ARIP C+ C WL L +LC R N H + HYRE + +A+
Sbjct: 28 ARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLG 87
Query: 100 DLSVWCFACHAYLNAQAIL 118
++ ++Y +L
Sbjct: 88 TITPDGADVYSYDEDDMVL 106
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain
Length = 126
Score = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 65 WLCLCCKEVLCSRYVN-KHMLRHY---REKNHSVALDYSDLSVWCFACHAYLNAQAILQL 120
WLCL C C R +H L+HY R + H + L + SVWC+ C + + QL
Sbjct: 55 WLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQL 114
Query: 121 RPVHETSYVLK 131
V YV K
Sbjct: 115 GQV--VDYVRK 123
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 198 WLCLCCKEVLCSRYVN-KHMLQHY---QETNHSVALGYSDLSVWCFAC 241
WLCL C C R +H L+HY + H + L + SVWC+ C
Sbjct: 55 WLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVC 102
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 14/81 (17%)
Query: 155 GAESGSVRHLTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGNWLCLCCKEVLCSRYV-- 212
G+ S +LT D+ V RIP C RC WL L VLC ++
Sbjct: 1 GSVSKYANNLTQLDNGV--------RIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFD 52
Query: 213 ----NKHMLQHYQETNHSVAL 229
N H L+HY++ + +A+
Sbjct: 53 SSGGNGHALEHYRDMGYPLAV 73
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 6/63 (9%)
Query: 46 ARIPTPDTPCNMCKHPRGNWLCLCCKEVLCSRYV------NKHMLRHYREKNHSVALDYS 99
RIP C C WL L VLC ++ N H L HYR+ + +A+
Sbjct: 17 VRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLG 76
Query: 100 DLS 102
++
Sbjct: 77 TIT 79
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 160 SVRHLTSCDHLVASLSTDLARIPNPDTPCNRCQHPRGN-WLCL--CCKEVLCSRYVNKHM 216
SV +T D + SL T C C+ N W CL C V C H
Sbjct: 11 SVGEITKEDLIQKSLGT-----------CQDCKVQGPNLWACLENRCSYVGCGESQVDHS 59
Query: 217 LQHYQETNHSVALGYSDLSVWCFAC 241
H QET H + + + L VWC+AC
Sbjct: 60 TIHSQETKHYLTVNLTTLRVWCYAC 84
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 54 PCNMCKHPRGN-WLCL--CCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFAC 108
C CK N W CL C V C H H +E H + ++ + L VWC+AC
Sbjct: 27 TCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHSQETKHYLTVNLTTLRVWCYAC 84
>pdb|1EYS|C Chain C, Crystal Structure Of Photosynthetic Reaction Center From A
Thermophilic Bacterium, Thermochromatium Tepidum
Length = 382
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 17/97 (17%)
Query: 50 TPDTPCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACH 109
+P CN C P GNW + + ++ V++ M R N ++ V C+ CH
Sbjct: 80 SPKEGCNYCHVP-GNW----ASDDIYTKVVSRRMFELVRAANSDWKAHVAETGVTCYTCH 134
Query: 110 AYLNAQAILQLRPVHETSYVLKFGRALPFN---TGQH 143
+ PV + ++V G P TGQ+
Sbjct: 135 ---------RGNPVPKYAWVTDPGPKYPSGLKPTGQN 162
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 183 NPDTPCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACH 242
+P CN C P GNW + + ++ V++ M + + N ++ V C+ CH
Sbjct: 80 SPKEGCNYCHVP-GNW----ASDDIYTKVVSRRMFELVRAANSDWKAHVAETGVTCYTCH 134
Query: 243 AYLNAQAILQLQPVHETAYVLKFGRALP 270
+ PV + A+V G P
Sbjct: 135 ---------RGNPVPKYAWVTDPGPKYP 153
>pdb|4AAY|A Chain A, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|C Chain C, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|E Chain E, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|G Chain G, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
Length = 845
Score = 28.1 bits (61), Expect = 5.6, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 17 DEMMIGGELGWVRHLASCDHLVASLSS 43
D+++IGG+ G V H+ CDH +L++
Sbjct: 471 DQLLIGGQ-GGVHHIWGCDHYKTTLNA 496
>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 = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 24/59 (40%)
Query: 187 PCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYL 245
C C +C + C + + H L H ++ H + ++ ++CF C Y+
Sbjct: 50 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 25/59 (42%)
Query: 54 PCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYL 112
C C +C + C + + H L H ++ H ++ ++ ++CF C Y+
Sbjct: 50 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 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 = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 24/59 (40%)
Query: 187 PCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYL 245
C C +C + C + + H L H ++ H + ++ ++CF C Y+
Sbjct: 50 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 25/59 (42%)
Query: 54 PCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYL 112
C C +C + C + + H L H ++ H ++ ++ ++CF C Y+
Sbjct: 50 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 108
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 24/59 (40%)
Query: 187 PCNRCQHPRGNWLCLCCKEVLCSRYVNKHMLQHYQETNHSVALGYSDLSVWCFACHAYL 245
C C +C + C + + H L H ++ H + ++ ++CF C Y+
Sbjct: 45 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 103
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 25/59 (42%)
Query: 54 PCNMCKHPRGNWLCLCCKEVLCSRYVNKHMLRHYREKNHSVALDYSDLSVWCFACHAYL 112
C C +C + C + + H L H ++ H ++ ++ ++CF C Y+
Sbjct: 45 KCGTCHEINSGATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYI 103
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
0.323 0.136 0.453
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,953,579
Number of Sequences: 62578
Number of extensions: 364505
Number of successful extensions: 923
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 896
Number of HSP's gapped (non-prelim): 26
length of query: 279
length of database: 14,973,337
effective HSP length: 98
effective length of query: 181
effective length of database: 8,840,693
effective search space: 1600165433
effective search space used: 1600165433
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (24.3 bits)