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= 009986
(521 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 88/359 (24%), Positives = 150/359 (41%), Gaps = 39/359 (10%)
Query: 192 VGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPE--------NYRHCKSPLVHRFGDLTRK 243
GL N+ T F+N +Q L PL ++FL E N K + + +L ++
Sbjct: 9 CGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQ 68
Query: 244 IWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSI 303
+W R+ V+P F V + + + F Q + E +++LL+ LH DL KK +
Sbjct: 69 MWSGRD--AHVAPRMFKTQVGRFAPQ-FSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYL 125
Query: 304 IYECFQG--ELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRXXXXXX--XXXX 359
+ G + V KE +N ND G + E ++
Sbjct: 126 ELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLT 185
Query: 360 XXXXXXKD-VMEKNII-PQ------VPLFNILKKFDG-ETVTE--------VVRPHVARM 402
KD VME ++ PQ V L + ++ F ET+ E + A
Sbjct: 186 LPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATK 245
Query: 403 RYRVTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSK- 461
++ + LPK +++H++RF+ N ++ +K T+V FP++ L + +++ N R
Sbjct: 246 KFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVC------NLSARPYV 299
Query: 462 YDLIANIVHDGKPEGGFYRVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYEQQ 520
YDLIA H G G Y + + K WY D +VS + Y+ Y+++
Sbjct: 300 YDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRR 358
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 71/159 (44%), Gaps = 15/159 (9%)
Query: 369 MEKNIIPQVPLFNILKKFDGETVTE---------VVRPHVARMRYRVTRLPKYMILHMRR 419
+ K P+V L + ++ F E V + ++ + R PK ++LH++R
Sbjct: 214 IAKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 273
Query: 420 FTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFY 479
F+++ K T VNFP+++L+L+++ EN + Y+L A H G GG Y
Sbjct: 274 FSESRIRTSKLTTFVNFPLRDLDLREFA-----SENTN-HAVYNLYAVSNHSGTTMGGHY 327
Query: 480 RVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYE 518
+ + W+ D V+ V S+ Y+ YE
Sbjct: 328 TAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 366
>pdb|3V6C|A Chain A, Crystal Structure Of Usp2 In Complex With Mutated
Ubiquitin
pdb|3V6E|A Chain A, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin
Length = 367
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 71/159 (44%), Gaps = 15/159 (9%)
Query: 369 MEKNIIPQVPLFNILKKFDGETVTE---------VVRPHVARMRYRVTRLPKYMILHMRR 419
+ K P+V L + ++ F E V + ++ + R PK ++LH++R
Sbjct: 207 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 266
Query: 420 FTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFY 479
F+++ K T VNFP+++L+L+++ EN + Y+L A H G GG Y
Sbjct: 267 FSESRIRTSKLTTFVNFPLRDLDLREF-----ASENTN-HAVYNLYAVSNHSGTTMGGHY 320
Query: 480 RVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYE 518
+ + W+ D V+ V S+ Y+ YE
Sbjct: 321 TAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 359
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 71/159 (44%), Gaps = 15/159 (9%)
Query: 369 MEKNIIPQVPLFNILKKFDGETVTE---------VVRPHVARMRYRVTRLPKYMILHMRR 419
+ K P+V L + ++ F E V + ++ + R PK ++LH++R
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 420 FTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFY 479
F+++ K T VNFP+++L+L+++ EN + Y+L A H G GG Y
Sbjct: 248 FSESRIRTSKLTTFVNFPLRDLDLREF-----ASENTN-HAVYNLYAVSNHSGTTMGGHY 301
Query: 480 RVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYE 518
+ + W+ D V+ V S+ Y+ YE
Sbjct: 302 TAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 71/159 (44%), Gaps = 15/159 (9%)
Query: 369 MEKNIIPQVPLFNILKKFDGETVTE---------VVRPHVARMRYRVTRLPKYMILHMRR 419
+ K P+V L + ++ F E V + ++ + R PK ++LH++R
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 420 FTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFY 479
F+++ K T VNFP+++L+L+++ EN + Y+L A H G GG Y
Sbjct: 248 FSESRIRTSKLTTFVNFPLRDLDLREF-----ASENTN-HAVYNLYAVSNHSGTTMGGHY 301
Query: 480 RVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYE 518
+ + W+ D V+ V S+ Y+ YE
Sbjct: 302 TAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 62/116 (53%), Gaps = 13/116 (11%)
Query: 389 ETVTEVVRPHVARMRYR--------VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKN 440
E +T+ R + + R R + +LP +++H++RF+ + + +K T V+FP++N
Sbjct: 261 EKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLEN 320
Query: 441 LELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVFVQRKSEELWYEMQD 496
L+L Y+ PK N K KY+L + H G +GG Y + + + + W++ D
Sbjct: 321 LDLSQYV--IGPKNNLK---KYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDD 371
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 62/116 (53%), Gaps = 13/116 (11%)
Query: 389 ETVTEVVRPHVARMRYR--------VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKN 440
E +T+ R + + R R + +LP +++H++RF+ + + +K T V+FP++N
Sbjct: 261 EKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLEN 320
Query: 441 LELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVFVQRKSEELWYEMQD 496
L+L Y+ PK N K KY+L + H G +GG Y + + + + W++ D
Sbjct: 321 LDLSQYV--IGPKNNLK---KYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDD 371
>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 = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 52/116 (44%), Gaps = 8/116 (6%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 263 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 316
Query: 466 ANIVHDGKPEGGFYRVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYEQQQ 521
A H G G Y + + W+ D VS VA SE Y+ Y+ Q
Sbjct: 317 ALCNHSGSVHYGHYTALC--RCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQ 370
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 11/111 (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 294
+WH + + V+P F +AV + F Q + EF+ L+ LH ++
Sbjct: 80 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEI 128
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 52/116 (44%), Gaps = 8/116 (6%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 257 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 310
Query: 466 ANIVHDGKPEGGFYRVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYEQQQ 521
A H G G Y + + W+ D VS VA SE Y+ Y+ Q
Sbjct: 311 ALCNHSGSVHYGHYTALC--RCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQ 364
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 11/111 (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 294
+WH + + V+P F +AV + F Q + EF+ L+ LH ++
Sbjct: 74 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEI 122
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 52/116 (44%), Gaps = 8/116 (6%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 244 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 297
Query: 466 ANIVHDGKPEGGFYRVFVQRKSEELWYEMQDLHVSETLPQMVALSETYMQIYEQQQ 521
A H G G Y + + W+ D VS VA SE Y+ Y+ Q
Sbjct: 298 ALCNHSGSVHYGHYTALC--RCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQ 351
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 11/111 (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 294
+WH + + V+P F +AV + F Q + EF+ L+ LH ++
Sbjct: 61 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEI 109
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
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 THSLEAGHHVYINLRTEKVYC 174
HS E H++ +NL T +V+C
Sbjct: 61 IHSQETKHYLTVNLTTLRVWC 81
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 36.2 bits (82), Expect = 0.048, 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 = 34.3 bits (77), Expect = 0.15, 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|2AYN|A Chain A, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|B Chain B, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|C Chain C, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYO|A Chain A, Structure Of Usp14 Bound To Ubquitin Aldehyde
Length = 404
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 39/155 (25%), Positives = 56/155 (36%), Gaps = 63/155 (40%)
Query: 405 RVTRLPKYMILHMRRFTKNNFFVEKNPT------LVNFPVKNLELKDYIPLPTPKENEKL 458
+++RLP Y+ + M RF F+ EK V FP+ + D L TP+ EK+
Sbjct: 226 KISRLPAYLTIQMVRF----FYKEKESVNAKVLKDVKFPL----MLDMYELCTPELQEKM 277
Query: 459 ---RSK--------------------------------------------YDLIANIVHD 471
RSK YDL A + H
Sbjct: 278 VSFRSKFKDLEDKKVNQQPNTSDKKSSPQKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQ 337
Query: 472 GK-PEGGFYRVFVQRKSEELWYEMQDLHVSETLPQ 505
G+ G Y +V+RK +E W + D VS P+
Sbjct: 338 GRSSSSGHYVSWVKRKQDE-WIKFDDDKVSIVTPE 371
>pdb|1NB8|A Chain A, Structure Of The Catalytic Domain Of Usp7 (Hausp)
pdb|1NB8|B Chain B, Structure Of The Catalytic Domain Of Usp7 (Hausp)
Length = 353
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 57/138 (41%), Gaps = 15/138 (10%)
Query: 370 EKNIIPQVPLFNILKKFDGETVTEVVRPHV--ARMRYRVTRLPKYMILHMRRF-----TK 422
+KNI + +++ DG+ + + A + LP + L + RF T
Sbjct: 150 KKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTD 209
Query: 423 NNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVF 482
N + FP + L L +++ PK+ + Y L A +VH G GG Y V+
Sbjct: 210 QNIKINDR---FEFP-EQLPLDEFLQKTDPKDP----ANYILHAVLVHSGDNHGGHYVVY 261
Query: 483 VQRKSEELWYEMQDLHVS 500
+ K + W + D VS
Sbjct: 262 LNPKGDGKWCKFDDDVVS 279
>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 = 2.3, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 57/133 (42%), Gaps = 19/133 (14%)
Query: 136 CLVCGKYYQGRG------QKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPS---L 186
L +YY +G QK+ YT + HVY + + VY + Y N+P
Sbjct: 177 ILFALRYYSYKGIMGEETQKAELYTDT-----HVYYYEKIDGVYQMDYSYGENNPRPHMT 231
Query: 187 EDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWH 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|1NBF|A Chain A, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|B Chain B, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|E Chain E, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
Length = 353
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 57/138 (41%), Gaps = 15/138 (10%)
Query: 370 EKNIIPQVPLFNILKKFDGETVTEVVRPHV--ARMRYRVTRLPKYMILHMRRF-----TK 422
+KNI + +++ DG+ + + A + LP + L + RF T
Sbjct: 150 KKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTD 209
Query: 423 NNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVF 482
N + FP + L L +++ PK+ + Y L A +VH G GG Y V+
Sbjct: 210 QNIKINDR---FEFP-EQLPLDEFLQKTDPKDP----ANYILHAVLVHSGDNHGGHYVVY 261
Query: 483 VQRKSEELWYEMQDLHVS 500
+ K + W + D VS
Sbjct: 262 LNPKGDGKWCKFDDDVVS 279
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 34/138 (24%), Positives = 57/138 (41%), Gaps = 15/138 (10%)
Query: 370 EKNIIPQVPLFNILKKFDGETVTEVVRPHV--ARMRYRVTRLPKYMILHMRRF-----TK 422
+KNI + +++ DG+ + + A + LP + L + RF T
Sbjct: 319 KKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTD 378
Query: 423 NNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVF 482
N + FP + L L +++ PK+ + Y L A +VH G GG Y V+
Sbjct: 379 QNIKINDR---FEFP-EQLPLDEFLQKTDPKDP----ANYILHAVLVHSGDNHGGHYVVY 430
Query: 483 VQRKSEELWYEMQDLHVS 500
+ K + W + D VS
Sbjct: 431 LNPKGDGKWCKFDDDVVS 448
>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 = 30.0 bits (66), Expect = 3.4, 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|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
Length = 109
Score = 30.0 bits (66), Expect = 3.4, 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|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 = 6.0, 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
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
0.318 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,144,644
Number of Sequences: 62578
Number of extensions: 623778
Number of successful extensions: 1372
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1344
Number of HSP's gapped (non-prelim): 27
length of query: 521
length of database: 14,973,337
effective HSP length: 103
effective length of query: 418
effective length of database: 8,527,803
effective search space: 3564621654
effective search space used: 3564621654
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: 54 (25.4 bits)