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= 011215
(491 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 = 71.6 bits (174), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 82/330 (24%), Positives = 138/330 (41%), Gaps = 39/330 (11%)
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 YDLIANIVHDGKPEGGFYRVFVQRKSEELW 491
YDLIA H G G Y + + K W
Sbjct: 300 YDLIAVSNHYGAMGVGHYTAYAKNKLNGKW 329
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 60/132 (45%), Gaps = 15/132 (11%)
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 RVFVQRKSEELW 491
+ + W
Sbjct: 328 TAYCRSPGTGEW 339
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 59/111 (53%), Gaps = 13/111 (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 LELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVFVQRKSEELW 491
L+L Y+ PK N K KY+L + H G +GG Y + + + + W
Sbjct: 321 LDLSQYV--IGPKNNLK---KYNLFSVSNHYGGLDGGHYTAYCKNAARQRW 366
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 32/111 (28%), Positives = 59/111 (53%), Gaps = 13/111 (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 LELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVFVQRKSEELW 491
L+L Y+ PK N K KY+L + H G +GG Y + + + + W
Sbjct: 321 LDLSQYV--IGPKNNLK---KYNLFSVSNHYGGLDGGHYTAYCKNAARQRW 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 = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 60/132 (45%), Gaps = 15/132 (11%)
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 RVFVQRKSEELW 491
+ + W
Sbjct: 321 TAYCRSPGTGEW 332
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 32/126 (25%), Positives = 58/126 (46%), Gaps = 15/126 (11%)
Query: 375 PQVPLFNILKKFDGETVTE---------VVRPHVARMRYRVTRLPKYMILHMRRFTKNNF 425
P+V L + ++ F E V + ++ + R PK ++LH++RF+++
Sbjct: 194 PEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRI 253
Query: 426 FVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLIANIVHDGKPEGGFYRVFVQR 485
K T VNFP+++L+L+++ EN + Y+L A H G GG Y + +
Sbjct: 254 RTSKLTTFVNFPLRDLDLREF-----ASENTN-HAVYNLYAVSNHSGTTMGGHYTAYCRS 307
Query: 486 KSEELW 491
W
Sbjct: 308 PGTGEW 313
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 60/132 (45%), Gaps = 15/132 (11%)
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 RVFVQRKSEELW 491
+ + W
Sbjct: 302 TAYCRSPGTGEW 313
>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 = 49.7 bits (117), Expect = 3e-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
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 263 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 316
Query: 466 ANIVHDGKPEGGFYRVFVQ 484
A H G G Y +
Sbjct: 317 ALCNHSGSVHYGHYTALCR 335
>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 = 49.7 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
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 257 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 310
Query: 466 ANIVHDGKPEGGFYRVFVQ 484
A H G G Y +
Sbjct: 311 ALCNHSGSVHYGHYTALCR 329
>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 = 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
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 406 VTRLPKYMILHMRRFTKNNFFVEKNPTLVNFPVKNLELKDYIPLPTPKENEKLRSKYDLI 465
V R P+ ++LH+ RF+ + ++K+ V+FP++ L L D+ ++ Y L
Sbjct: 244 VQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF------ASDKAGSPVYQLY 297
Query: 466 ANIVHDGKPEGGFYRVFVQ 484
A H G G Y +
Sbjct: 298 ALCNHSGSVHYGHYTALCR 316
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
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 = 36.2 bits (82), Expect = 0.047, 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 = 0.14, 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 = 2.2, 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|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 = 3.2, 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 = 3.2, 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 = 5.5, 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|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 = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
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 VQRKSEELW 491
+ K + W
Sbjct: 262 LNPKGDGKW 270
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 28.5 bits (62), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
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 VQRKSEELW 491
+ K + W
Sbjct: 431 LNPKGDGKW 439
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 0.137 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,372,041
Number of Sequences: 62578
Number of extensions: 588885
Number of successful extensions: 1274
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1250
Number of HSP's gapped (non-prelim): 26
length of query: 491
length of database: 14,973,337
effective HSP length: 103
effective length of query: 388
effective length of database: 8,527,803
effective search space: 3308787564
effective search space used: 3308787564
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)