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= 016557
(387 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MTN|A Chain A, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
pdb|3MTN|C Chain C, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
Length = 373
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 12/122 (9%)
Query: 191 HVGLNNIKETDFVNVTIQSLMRVTPLRNFFL-------IPENYRHCKSPLVHRFGDLTRK 243
HVGL N+ T F+N +Q L PLR+F L +P R L F D+
Sbjct: 22 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGR--AQELTEAFADVIGA 79
Query: 244 IWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTS 302
+WH + + V+P F +AV + F Q + EF+ L+ LH ++ R ++
Sbjct: 80 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 137
Query: 303 II 304
I+
Sbjct: 138 IL 139
>pdb|2Y5B|A Chain A, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
pdb|2Y5B|E Chain E, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
Length = 370
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 12/122 (9%)
Query: 191 HVGLNNIKETDFVNVTIQSLMRVTPLRNFFL-------IPENYRHCKSPLVHRFGDLTRK 243
HVGL N+ T F+N +Q L PLR+F L +P R L F D+
Sbjct: 16 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGR--AQELTEAFADVIGA 73
Query: 244 IWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTS 302
+WH + + V+P F +AV + F Q + EF+ L+ LH ++ R ++
Sbjct: 74 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 131
Query: 303 II 304
I+
Sbjct: 132 IL 133
>pdb|3I3T|A Chain A, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|C Chain C, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|E Chain E, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|G Chain G, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
Length = 355
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 12/122 (9%)
Query: 191 HVGLNNIKETDFVNVTIQSLMRVTPLRNFFL-------IPENYRHCKSPLVHRFGDLTRK 243
HVGL N+ T F+N +Q L PLR+F L +P R L F D+
Sbjct: 3 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGR--AQELTEAFADVIGA 60
Query: 244 IWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTS 302
+WH + + V+P F +AV + F Q + EF+ L+ LH ++ R ++
Sbjct: 61 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 118
Query: 303 II 304
I+
Sbjct: 119 IL 120
>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
Length = 367
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/115 (28%), Positives = 54/115 (46%), Gaps = 11/115 (9%)
Query: 193 GLNNIKETDFVNVTIQSLMRVTPLRNFFLIPE--------NYRHCKSPLVHRFGDLTRKI 244
GL N+ T F+N +Q L PL ++FL E N K + + +L +++
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQM 69
Query: 245 WHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKK 299
W R+ V+P F V + + + F Q + E +++LL+ LH DL KK
Sbjct: 70 WSGRD--AHVAPRMFKTQVGRFAPQ-FSGYQQQDSQELLAFLLDGLHEDLNRVKK 121
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 10/88 (11%)
Query: 102 RRDCPYLDTVNRQVLDFDFEKF------CSVSLSNLNVYACLV--CGKYYQGRGQKSHAY 153
R CP+LD+V + +K C V NL +ACL C G Q H+
Sbjct: 3 RNHCPHLDSVGEITKEDLIQKSLGTCQDCKVQGPNL--WACLENRCSYVGCGESQVDHST 60
Query: 154 THSLEAGHHVYINLRTEKVYCLPDGYEI 181
HS E H++ +NL T +V+C E+
Sbjct: 61 IHSQETKHYLTVNLTTLRVWCYACSKEV 88
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 137 LVCGK-YYQGRGQKSHAYTHSLEAGHHVYINLRT-----EKVYCLPDGYEINDPSL-EDI 189
++CG+ Y+ G G +HA H E G+ + + L T VY + + DPSL E +
Sbjct: 236 ILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHL 295
Query: 190 RHVGLNNIK 198
H G++ +K
Sbjct: 296 SHFGIDMLK 304
>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 = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 137 LVCGK-YYQGRGQKSHAYTHSLEAGHHVYINLRT-----EKVYCLPDGYEINDPSL-EDI 189
++CG+ Y+ G G +HA H E G+ + + L T VY + + DPSL E +
Sbjct: 55 ILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHL 114
Query: 190 RHVGLNNIK 198
H G++ +K
Sbjct: 115 SHFGIDMLK 123
>pdb|2JES|A Chain A, Portal Protein From Bacteriophage Spp1
pdb|2JES|C Chain C, Portal Protein From Bacteriophage Spp1
pdb|2JES|E Chain E, Portal Protein From Bacteriophage Spp1
pdb|2JES|G Chain G, Portal Protein From Bacteriophage Spp1
pdb|2JES|I Chain I, Portal Protein From Bacteriophage Spp1
pdb|2JES|K Chain K, Portal Protein From Bacteriophage Spp1
pdb|2JES|M Chain M, Portal Protein From Bacteriophage Spp1
pdb|2JES|O Chain O, Portal Protein From Bacteriophage Spp1
pdb|2JES|Q Chain Q, Portal Protein From Bacteriophage Spp1
pdb|2JES|S Chain S, Portal Protein From Bacteriophage Spp1
pdb|2JES|U Chain U, Portal Protein From Bacteriophage Spp1
pdb|2JES|W Chain W, Portal Protein From Bacteriophage Spp1
pdb|2JES|Y Chain Y, Portal Protein From Bacteriophage Spp1
Length = 503
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 56/133 (42%), Gaps = 19/133 (14%)
Query: 136 CLVCGKYYQGRG------QKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDI 189
L +YY +G QK+ YT + HVY + + VY + Y N+P
Sbjct: 177 ILFALRYYSYKGIMGEETQKAELYTDT-----HVYYYEKIDGVYQMDYSYGENNPRPHMT 231
Query: 190 R---HVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWH 246
+ +G + F N + V+ L+ + + +NY S + F D + ++
Sbjct: 232 KGGQAIGWGRVPIIPFKN----NEEMVSDLKFYKDLIDNYDSITSSTMDSFSDFQQIVYV 287
Query: 247 ARNFKGQVSPHEF 259
+N+ G+ +P EF
Sbjct: 288 LKNYDGE-NPKEF 299
>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
Length = 109
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 134 YACLVCGKYYQGRGQKSHAYTHSLEAGHHV---YINLRTEKVYCLPDGYEINDPSLEDIR 190
+ CL C + Y GR H H +GH + YI+L YC Y ++ +L D++
Sbjct: 37 WVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYC--QAY-VHHQALLDVK 93
Query: 191 HVGLNN 196
++ N
Sbjct: 94 NIAHQN 99
>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 = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 134 YACLVCGKYYQGRGQKSHAYTHSLEAGHHV---YINLRTEKVYCLPDGYEINDPSLEDIR 190
+ CL C + Y GR H H +GH + YI+L YC Y ++ +L D++
Sbjct: 35 WVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYC--QAY-VHHQALLDVK 91
Query: 191 HVGLNN 196
++ N
Sbjct: 92 NIAHQN 97
>pdb|3IUF|A Chain A, Crystal Structure Of The C2h2-Type Zinc Finger Domain Of
Human Ubi-D4
Length = 48
Score = 29.3 bits (64), Expect = 4.4, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 134 YACLVCGKYYQGRGQKSHAYTHS 156
YAC +CGK Y+ R S+ Y HS
Sbjct: 8 YACDICGKRYKNRPGLSYHYAHS 30
>pdb|3RON|A Chain A, Crystal Structure And Hemolytic Activity Of The Cyt1aa
Toxin From Bacillus Thuringiensis Subsp. Israelensis
pdb|3RON|B Chain B, Crystal Structure And Hemolytic Activity Of The Cyt1aa
Toxin From Bacillus Thuringiensis Subsp. Israelensis
Length = 249
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 172 VYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPL 216
+YC+P G+EI ++++ V I+++ NV IQSL PL
Sbjct: 188 MYCVPVGFEIKVSAVKE--QVLFFTIQDSASYNVNIQSLKFAQPL 230
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 0.135 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,058,879
Number of Sequences: 62578
Number of extensions: 435008
Number of successful extensions: 918
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 910
Number of HSP's gapped (non-prelim): 13
length of query: 387
length of database: 14,973,337
effective HSP length: 101
effective length of query: 286
effective length of database: 8,652,959
effective search space: 2474746274
effective search space used: 2474746274
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)