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= 003370
(825 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 = 263 bits (671), Expect = 4e-70, Method: Compositional matrix adjust.
Identities = 124/184 (67%), Positives = 145/184 (78%), Gaps = 1/184 (0%)
Query: 222 NLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLWSS 280
NLGNT FMNSALQCL +T L YFL D Y EIN +NPLGM GE+A A+ +L++++WS
Sbjct: 13 NLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSG 72
Query: 281 GRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDSGG 340
A VAPR FK ++ RFAPQFSGY Q DSQELLAFLLDGLHEDLNRVK+KPY+E+KD+ G
Sbjct: 73 RDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANG 132
Query: 341 RPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPLPSTV 400
RPD VA E W+NH+ RNDS+IVD F G +KSTLVCP C+KVS+TFDPF YLTLPLP
Sbjct: 133 RPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKK 192
Query: 401 TRTM 404
R M
Sbjct: 193 DRVM 196
Score = 190 bits (482), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 87/154 (56%), Positives = 112/154 (72%)
Query: 654 KKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRF 713
+K ++ ++L C++ F T E LG D WYCP CK+H+QATKK DLW LP +LV HLKRF
Sbjct: 204 QKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRF 263
Query: 714 SYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGGHYTAYAKL 773
SY+RY ++KLDT V FPI L++S+++ + YVYDL A+SNHYG +G GHYTAYAK
Sbjct: 264 SYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKN 323
Query: 774 IDENRWYHFDDSHVSPVSEGDIKTSAAYVLFYRR 807
+WY+FDDS+VS SE I T AAYVLFY+R
Sbjct: 324 KLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQR 357
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 179 bits (455), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 88/185 (47%), Positives = 122/185 (65%), Gaps = 1/185 (0%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLWS 279
+NLGNTC+MNS LQCL + P LA YF + Y D+IN N LG GE+A FG +++ LW+
Sbjct: 66 RNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWT 125
Query: 280 SGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDSG 339
++P+ FK + + QF+GY+Q DSQELL FL+DGLHEDLN+ + + +++
Sbjct: 126 GQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENND 185
Query: 340 GRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPLPST 399
D + A W+ HK N+S+IV +FQGQ+KST+ C C K S TF+ FMYL+LPL ST
Sbjct: 186 HLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLAST 245
Query: 400 VTRTM 404
T+
Sbjct: 246 SKCTL 250
Score = 138 bits (348), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 72/144 (50%), Positives = 94/144 (65%)
Query: 662 SLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRFSYSRYLKN 721
+L CL F EE L ++ +YC C+ R + KK+++W LP VL+ HLKRFSY K
Sbjct: 249 TLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQ 308
Query: 722 KLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGGHYTAYAKLIDENRWYH 781
KL T V+FP+ NLDLS+Y+ Y+LF++SNHYGGL GGHYTAY K RW+
Sbjct: 309 KLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFK 368
Query: 782 FDDSHVSPVSEGDIKTSAAYVLFY 805
FDD VS +S +K+SAAY+LFY
Sbjct: 369 FDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 172 bits (436), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 86/185 (46%), Positives = 118/185 (63%), Gaps = 1/185 (0%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLWS 279
+NLGNTC+ NS LQCL + P LA YF + Y D+IN N LG GE+A FG + + LW+
Sbjct: 66 RNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIXKALWT 125
Query: 280 SGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDSG 339
++P+ FK + + QF+GY+Q DSQELL FL DGLHEDLN+ + + +++
Sbjct: 126 GQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEENND 185
Query: 340 GRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPLPST 399
D + A W+ HK N+S+IV +FQGQ+KST+ C C K S TF+ F YL+LPL ST
Sbjct: 186 HLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLAST 245
Query: 400 VTRTM 404
T+
Sbjct: 246 SKCTL 250
Score = 138 bits (348), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 72/144 (50%), Positives = 94/144 (65%)
Query: 662 SLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRFSYSRYLKN 721
+L CL F EE L ++ +YC C+ R + KK+++W LP VL+ HLKRFSY K
Sbjct: 249 TLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQ 308
Query: 722 KLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGGHYTAYAKLIDENRWYH 781
KL T V+FP+ NLDLS+Y+ Y+LF++SNHYGGL GGHYTAY K RW+
Sbjct: 309 KLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFK 368
Query: 782 FDDSHVSPVSEGDIKTSAAYVLFY 805
FDD VS +S +K+SAAY+LFY
Sbjct: 369 FDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 147 bits (372), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 78/178 (43%), Positives = 107/178 (60%), Gaps = 4/178 (2%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLW- 278
+NLGNTCFMNS LQCL +T +L Y L Y +++ + H L F L++ +W
Sbjct: 13 RNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS--NAHTALVEEFAKLIQTIWT 70
Query: 279 SSGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDS 338
SS V+P FK ++ R+AP+F GYNQ D+QE L FLLDGLH ++NRV +P ++
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 339 GGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPL 396
PD+E + W+ + R DS I D+F GQ KS+L C C S FDPF L+LP+
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 188
Score = 120 bits (302), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 69/184 (37%), Positives = 105/184 (57%), Gaps = 9/184 (4%)
Query: 634 LYDPSYIKDLPVVHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQA 693
++DP + LP+ K G+ ++L C+ F E+ L D+ C +C+ ++
Sbjct: 177 VFDPFWDLSLPIA-KRGY-------PEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 228
Query: 694 TKKLDLWMLPDVLVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLF 753
KK + P +LV HLKRFS SR +KL TFVNFP+ +LDL ++ S++ VY+L+
Sbjct: 229 IKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREF-ASENTNHAVYNLY 287
Query: 754 AISNHYGGLGGGHYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFYRRVKSKTK 813
A+SNH G GGHYTAY + W+ F+DS V+P+S ++TS AY+LFY ++
Sbjct: 288 AVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSR 347
Query: 814 AEMA 817
A
Sbjct: 348 MAAA 351
>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 = 147 bits (372), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 78/178 (43%), Positives = 107/178 (60%), Gaps = 4/178 (2%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLW- 278
+NLGNTCFMNS LQCL +T +L Y L Y +++ + H L F L++ +W
Sbjct: 32 RNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS--NAHTALVEEFAKLIQTIWT 89
Query: 279 SSGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDS 338
SS V+P FK ++ R+AP+F GYNQ D+QE L FLLDGLH ++NRV +P ++
Sbjct: 90 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 149
Query: 339 GGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPL 396
PD+E + W+ + R DS I D+F GQ KS+L C C S FDPF L+LP+
Sbjct: 150 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 207
Score = 120 bits (301), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 68/172 (39%), Positives = 102/172 (59%), Gaps = 9/172 (5%)
Query: 634 LYDPSYIKDLPVVHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQA 693
++DP + LP+ K G+ ++L C+ F E+ L D+ C +C+ ++
Sbjct: 196 VFDPFWDLSLPIA-KRGY-------PEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 247
Query: 694 TKKLDLWMLPDVLVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLF 753
KK + P +LV HLKRFS SR +KL TFVNFP+ +LDL ++ S++ VY+L+
Sbjct: 248 IKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREF-ASENTNHAVYNLY 306
Query: 754 AISNHYGGLGGGHYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
A+SNH G GGHYTAY + W+ F+DS V+P+S ++TS AY+LFY
Sbjct: 307 AVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 147 bits (371), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 78/178 (43%), Positives = 107/178 (60%), Gaps = 4/178 (2%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLW- 278
+NLGNTCFMNS LQCL +T +L Y L Y +++ + H L F L++ +W
Sbjct: 39 RNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS--NAHTALVEEFAKLIQTIWT 96
Query: 279 SSGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDS 338
SS V+P FK ++ R+AP+F GYNQ D+QE L FLLDGLH ++NRV +P ++
Sbjct: 97 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 156
Query: 339 GGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPL 396
PD+E + W+ + R DS I D+F GQ KS+L C C S FDPF L+LP+
Sbjct: 157 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 214
Score = 119 bits (299), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 68/172 (39%), Positives = 101/172 (58%), Gaps = 9/172 (5%)
Query: 634 LYDPSYIKDLPVVHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQA 693
++DP + LP+ K G+ ++L C+ F E+ L D C +C+ ++
Sbjct: 203 VFDPFWDLSLPIA-KRGY-------PEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRC 254
Query: 694 TKKLDLWMLPDVLVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLF 753
KK + P +LV HLKRFS SR +KL TFVNFP+ +LDL ++ S++ VY+L+
Sbjct: 255 IKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREF-ASENTNHAVYNLY 313
Query: 754 AISNHYGGLGGGHYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
A+SNH G GGHYTAY + W+ F+DS V+P+S ++TS AY+LFY
Sbjct: 314 AVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 365
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 144 bits (362), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 77/178 (43%), Positives = 106/178 (59%), Gaps = 4/178 (2%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGD-YSDEINTENPLGMHGELALAFGDLLRKLW- 278
+NLGNT FMNS LQCL +T +L Y L Y +++ + H L F L++ +W
Sbjct: 13 RNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS--NAHTALVEEFAKLIQTIWT 70
Query: 279 SSGRAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEMKDS 338
SS V+P FK ++ R+AP+F GYNQ D+QE L FLLDGLH ++NRV +P ++
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 339 GGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSITFDPFMYLTLPL 396
PD+E + W+ + R DS I D+F GQ KS+L C C S FDPF L+LP+
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 188
Score = 120 bits (301), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 68/172 (39%), Positives = 102/172 (59%), Gaps = 9/172 (5%)
Query: 634 LYDPSYIKDLPVVHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQA 693
++DP + LP+ K G+ ++L C+ F E+ L D+ C +C+ ++
Sbjct: 177 VFDPFWDLSLPIA-KRGY-------PEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 228
Query: 694 TKKLDLWMLPDVLVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLF 753
KK + P +LV HLKRFS SR +KL TFVNFP+ +LDL ++ S++ VY+L+
Sbjct: 229 IKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREF-ASENTNHAVYNLY 287
Query: 754 AISNHYGGLGGGHYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
A+SNH G GGHYTAY + W+ F+DS V+P+S ++TS AY+LFY
Sbjct: 288 AVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>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 = 120 bits (301), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 74/194 (38%), Positives = 100/194 (51%), Gaps = 20/194 (10%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLG-DYSDEINTENPLGMHGELALAFGDLLRKLWS 279
+NLGNTCF+N+ LQCL T L + L D+ E+ G EL AF D++ LW
Sbjct: 20 RNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGG---GRAQELTEAFADVIGALWH 76
Query: 280 SGRA-AVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQK-------- 330
AV P F+ ++ P FSGY+Q D+QE L L++ LH ++NR ++
Sbjct: 77 PDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 136
Query: 331 PYIEMKDSGGR-------PDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS 383
P GG D++ AN WK + R DS IVD+F GQ KS L C C S
Sbjct: 137 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRS 196
Query: 384 ITFDPFMYLTLPLP 397
TF+ F L+LP+P
Sbjct: 197 TTFEVFCDLSLPIP 210
Score = 112 bits (281), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 63/161 (39%), Positives = 89/161 (55%), Gaps = 8/161 (4%)
Query: 646 VHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDV 705
+ K GF K +SL C + F EE L ++ C +C++ ++TKKL + P +
Sbjct: 209 IPKKGFAGGK-----VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRI 263
Query: 706 LVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGG 765
LV HL RFS SR K V+FP+ L L + K G S VY L+A+ NH G + G
Sbjct: 264 LVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQLYALCNHSGSVHYG 322
Query: 766 HYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFYR 806
HYTA + + W+ ++DS VSPVSE + +S YVLFY+
Sbjct: 323 HYTALCRC--QTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 361
>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 = 120 bits (301), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 74/194 (38%), Positives = 100/194 (51%), Gaps = 20/194 (10%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLG-DYSDEINTENPLGMHGELALAFGDLLRKLWS 279
+NLGNTCF+N+ LQCL T L + L D+ E+ G EL AF D++ LW
Sbjct: 7 RNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGG---GRAQELTEAFADVIGALWH 63
Query: 280 SGRA-AVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQK-------- 330
AV P F+ ++ P FSGY+Q D+QE L L++ LH ++NR ++
Sbjct: 64 PDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 123
Query: 331 PYIEMKDSGGR-------PDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS 383
P GG D++ AN WK + R DS IVD+F GQ KS L C C S
Sbjct: 124 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRS 183
Query: 384 ITFDPFMYLTLPLP 397
TF+ F L+LP+P
Sbjct: 184 TTFEVFCDLSLPIP 197
Score = 113 bits (282), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 63/161 (39%), Positives = 89/161 (55%), Gaps = 8/161 (4%)
Query: 646 VHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDV 705
+ K GF K +SL C + F EE L ++ C +C++ ++TKKL + P +
Sbjct: 196 IPKKGFAGGK-----VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRI 250
Query: 706 LVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGG 765
LV HL RFS SR K V+FP+ L L + K G S VY L+A+ NH G + G
Sbjct: 251 LVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQLYALCNHSGSVHYG 309
Query: 766 HYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFYR 806
HYTA + + W+ ++DS VSPVSE + +S YVLFY+
Sbjct: 310 HYTALCRC--QTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 348
>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 = 120 bits (300), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 74/194 (38%), Positives = 100/194 (51%), Gaps = 20/194 (10%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLG-DYSDEINTENPLGMHGELALAFGDLLRKLWS 279
+NLGNTCF+N+ LQCL T L + L D+ E+ G EL AF D++ LW
Sbjct: 26 RNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGG---GRAQELTEAFADVIGALWH 82
Query: 280 SGRA-AVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLDGLHEDLNRVKQK-------- 330
AV P F+ ++ P FSGY+Q D+QE L L++ LH ++NR ++
Sbjct: 83 PDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 142
Query: 331 PYIEMKDSGGR-------PDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS 383
P GG D++ AN WK + R DS IVD+F GQ KS L C C S
Sbjct: 143 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRS 202
Query: 384 ITFDPFMYLTLPLP 397
TF+ F L+LP+P
Sbjct: 203 TTFEVFCDLSLPIP 216
Score = 113 bits (282), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 63/161 (39%), Positives = 89/161 (55%), Gaps = 8/161 (4%)
Query: 646 VHKTGFTVKKTRQEAISLFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDV 705
+ K GF K +SL C + F EE L ++ C +C++ ++TKKL + P +
Sbjct: 215 IPKKGFAGGK-----VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRI 269
Query: 706 LVFHLKRFSYSRYLKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGG 765
LV HL RFS SR K V+FP+ L L + K G S VY L+A+ NH G + G
Sbjct: 270 LVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQLYALCNHSGSVHYG 328
Query: 766 HYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFYR 806
HYTA + + W+ ++DS VSPVSE + +S YVLFY+
Sbjct: 329 HYTALCRC--QTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 367
>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 = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 85/153 (55%), Gaps = 13/153 (8%)
Query: 663 LFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRFSYSRYLKN- 721
L+ CLD+F +E L D ++C +C + A K+L + LP VLV LKRF + N
Sbjct: 321 LYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 379
Query: 722 KLDTFVNFPILNLDLSKYMKSKDGESY---------VYDLFAISNHYGGLGGGHYTAYAK 772
KLD F+ FP L++ Y +K+ + + +Y+L I +H G + GHY A+ K
Sbjct: 380 KLDDFIEFPTY-LNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 438
Query: 773 LIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
I +W+ F+DS VS +S+ ++ AY+LFY
Sbjct: 439 -ISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 49/190 (25%), Positives = 87/190 (45%), Gaps = 35/190 (18%)
Query: 222 NLGNTCFMNSALQCLVHTPDLAQYFLGDYSDEINTENPLGMHGE--LALAFGDLLRKLW- 278
N+G+TCFM+S LQCL+H P YF+ +I++ N + + A ++ +L+
Sbjct: 146 NMGSTCFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 201
Query: 279 --------SSGRAAVAPRAFKGKLA---RFAPQFSGYNQHDSQELLAFLLDGLHEDLNRV 327
SS + F L + +GY+Q D+ E F+++ +H+
Sbjct: 202 ALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ----- 256
Query: 328 KQKPYIEMKDSGGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS-ITF 386
Y+ D A E + + + + ++ VF+G +S++VCP C S T
Sbjct: 257 ---SYV--------LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTI 305
Query: 387 DPFMYLTLPL 396
DPF+ L+L +
Sbjct: 306 DPFLDLSLDI 315
>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 = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 85/153 (55%), Gaps = 13/153 (8%)
Query: 663 LFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRFSYSRYLKN- 721
L+ CLD+F +E L D ++C +C + A K+L + LP VLV LKRF + N
Sbjct: 321 LYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 379
Query: 722 KLDTFVNFPILNLDLSKYMKSKDGESY---------VYDLFAISNHYGGLGGGHYTAYAK 772
KLD F+ FP L++ Y +K+ + + +Y+L I +H G + GHY A+ K
Sbjct: 380 KLDDFIEFPTY-LNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 438
Query: 773 LIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
I +W+ F+DS VS +S+ ++ AY+LFY
Sbjct: 439 -ISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/190 (26%), Positives = 87/190 (45%), Gaps = 35/190 (18%)
Query: 222 NLGNTCFMNSALQCLVHTPDLAQYFLGDYSDEINTENPLGMHGE--LALAFGDLLRKLW- 278
N+GNTCFM+S LQCL+H P YF+ +I++ N + + A ++ +L+
Sbjct: 146 NMGNTCFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 201
Query: 279 --------SSGRAAVAPRAFKGKLA---RFAPQFSGYNQHDSQELLAFLLDGLHEDLNRV 327
SS + F L + +GY+Q D+ E F+++ +H+
Sbjct: 202 ALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ----- 256
Query: 328 KQKPYIEMKDSGGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS-ITF 386
Y+ D A E + + + + ++ VF+G +S++VCP C S T
Sbjct: 257 ---SYV--------LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTI 305
Query: 387 DPFMYLTLPL 396
DPF+ L+L +
Sbjct: 306 DPFLDLSLDI 315
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 85/153 (55%), Gaps = 13/153 (8%)
Query: 663 LFSCLDAFLTEEPLGPDDMWYCPQCKEHRQATKKLDLWMLPDVLVFHLKRFSYSRYLKN- 721
L+ CLD+F +E L D ++C +C + A K+L + LP VLV LKRF + N
Sbjct: 316 LYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 374
Query: 722 KLDTFVNFPILNLDLSKYMKSKDGESY---------VYDLFAISNHYGGLGGGHYTAYAK 772
KLD F+ FP L++ Y +K+ + + +Y+L I +H G + GHY A+ K
Sbjct: 375 KLDDFIEFPTY-LNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 433
Query: 773 LIDENRWYHFDDSHVSPVSEGDIKTSAAYVLFY 805
I +W+ F+DS VS +S+ ++ AY+LFY
Sbjct: 434 -ISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 465
Score = 62.4 bits (150), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 49/190 (25%), Positives = 87/190 (45%), Gaps = 35/190 (18%)
Query: 222 NLGNTCFMNSALQCLVHTPDLAQYFLGDYSDEINTENPLGMHGE--LALAFGDLLRKLW- 278
N+G+TCFM+S LQCL+H P YF+ +I++ N + + A ++ +L+
Sbjct: 141 NMGSTCFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 196
Query: 279 --------SSGRAAVAPRAFKGKLA---RFAPQFSGYNQHDSQELLAFLLDGLHEDLNRV 327
SS + F L + +GY+Q D+ E F+++ +H+
Sbjct: 197 ALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ----- 251
Query: 328 KQKPYIEMKDSGGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVS-ITF 386
Y+ D A E + + + + ++ VF+G +S++VCP C S T
Sbjct: 252 ---SYV--------LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTI 300
Query: 387 DPFMYLTLPL 396
DPF+ L+L +
Sbjct: 301 DPFLDLSLDI 310
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 49.3 bits (116), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 56/120 (46%), Gaps = 25/120 (20%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLG-----------DYSDEINTENPLGMHGELALA 269
+NLGN+C++NS +Q L PD + ++ D + + +T+ HG L+
Sbjct: 348 RNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLS-- 405
Query: 270 FGDLLRKLWSSG-----------RAAVAPRAFKGKLARFAPQFSGYNQHDSQELLAFLLD 318
G+ + + SG + +APR FK + + P+FS Q D+QE L++
Sbjct: 406 -GEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLIN 464
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 59/134 (44%), Gaps = 13/134 (9%)
Query: 662 SLFSCLDAFLTEEPLGPDDMWYCPQCKEH--RQATKKLDLWMLPDVLVFHLKRFSYSRYL 719
++F ++ E L D+ + EH ++A K + LP VL L RF Y
Sbjct: 152 NIFESFVDYVAVEQLDGDNKY---DAGEHGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQT 208
Query: 720 KN--KLDTFVNFPILNLDLSKYMKS---KDGESYVYDLFAISNHYGGLGGGHYTAYAKLI 774
K++ FP L L ++++ KD +Y+ L A+ H G GGHY Y
Sbjct: 209 DQNIKINDRFEFP-EQLPLDEFLQKTDPKDPANYI--LHAVLVHSGDNHGGHYVVYLNPK 265
Query: 775 DENRWYHFDDSHVS 788
+ +W FDD VS
Sbjct: 266 GDGKWCKFDDDVVS 279
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 15/103 (14%)
Query: 221 QNLGNTCFMNSALQCLVHTPDL--AQYFLGDYSDEINTENPLGMHGELALAFGDLLRKLW 278
+N G TC+ NS LQ L T L A Y D+ + PL L++++
Sbjct: 10 KNQGATCYXNSLLQTLFFTNQLRKAVYXXPTEGDDSSKSVPLA------------LQRVF 57
Query: 279 SSGRAAVAPRAFKGKLARFA-PQFSGYNQHDSQELLAFLLDGL 320
+ + P K F + QHD QEL LLD +
Sbjct: 58 YELQHSDKPVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDNV 100
>pdb|3PV1|A Chain A, Crystal Structure Of The Usp15 Dusp-Ubl Domains
pdb|3PV1|B Chain B, Crystal Structure Of The Usp15 Dusp-Ubl Domains
Length = 225
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 60/115 (52%), Gaps = 4/115 (3%)
Query: 33 SFFVGGPALPRKMISEGI-VNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEK- 90
+ G + RK++ +G+ V +VEV+ LKL ++ + + V R KA T EK
Sbjct: 107 TLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKE 166
Query: 91 VCKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLEVQVDNG 144
+ K+ I EK R+W+ + + PL+ D T+ DA L Q +++E + ++G
Sbjct: 167 IRKIFSIPDEKETRLWNKY-MSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG 220
>pdb|3PPA|A Chain A, Structure Of The Dusp-Ubl Domains Of Usp15
Length = 237
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 60/115 (52%), Gaps = 4/115 (3%)
Query: 33 SFFVGGPALPRKMISEGI-VNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEK- 90
+ G + RK++ +G+ V +VEV+ LKL ++ + + V R KA T EK
Sbjct: 119 TLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKE 178
Query: 91 VCKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLEVQVDNG 144
+ K+ I EK R+W+ + + PL+ D T+ DA L Q +++E + ++G
Sbjct: 179 IRKIFSIPDEKETRLWNKY-MSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG 232
>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 = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 59/134 (44%), Gaps = 13/134 (9%)
Query: 662 SLFSCLDAFLTEEPLGPDDMWYCPQCKEH--RQATKKLDLWMLPDVLVFHLKRFSYSRYL 719
++F ++ E L D+ + EH ++A K + LP VL L RF Y
Sbjct: 152 NIFESFVDYVAVEQLDGDNKY---DAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQT 208
Query: 720 KN--KLDTFVNFPILNLDLSKYMKS---KDGESYVYDLFAISNHYGGLGGGHYTAYAKLI 774
K++ FP L L ++++ KD +Y+ L A+ H G GGHY Y
Sbjct: 209 DQNIKINDRFEFP-EQLPLDEFLQKTDPKDPANYI--LHAVLVHSGDNHGGHYVVYLNPK 265
Query: 775 DENRWYHFDDSHVS 788
+ +W FDD VS
Sbjct: 266 GDGKWCKFDDDVVS 279
Score = 36.2 bits (82), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 53/138 (38%), Gaps = 27/138 (19%)
Query: 221 QNLGNTCFMNSALQCLVHTPDL--AQYFLGDYSDEINTENPLGMHGELALAFGDLLRKLW 278
+N G TC+MNS LQ L T L A Y + D+ + PL L++++
Sbjct: 10 KNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLA------------LQRVF 57
Query: 279 SSGRAAVAPRAFKGKLARFA-PQFSGYNQHDSQELLAFLLDGLHEDLN------------ 325
+ + P K F + QHD QEL LLD + +
Sbjct: 58 YELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLF 117
Query: 326 RVKQKPYIEMKDSGGRPD 343
R K YI+ K+ R D
Sbjct: 118 RGKMVSYIQCKEVDYRSD 135
>pdb|4A3O|A Chain A, Crystal Structure Of The Usp15 Dusp-Ubl Monomer
pdb|4A3O|B Chain B, Crystal Structure Of The Usp15 Dusp-Ubl Monomer
Length = 220
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 60/115 (52%), Gaps = 4/115 (3%)
Query: 33 SFFVGGPALPRKMISEGI-VNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEK- 90
+ G + RK++ +G+ V +VEV+ LKL ++ + + V R KA T EK
Sbjct: 102 TLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKE 161
Query: 91 VCKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLEVQVDNG 144
+ K+ I EK R+W+ + + PL+ D T+ DA L Q +++E + ++G
Sbjct: 162 IRKIFSIPDEKETRLWNKY-MSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG 215
>pdb|3T9L|A Chain A, Structure Of N-Terminal Dusp-Ubl Domains Of Human Usp15
Length = 230
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 60/115 (52%), Gaps = 4/115 (3%)
Query: 33 SFFVGGPALPRKMISEGI-VNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEK- 90
+ G + RK++ +G+ V +VEV+ LKL ++ + + V R KA T EK
Sbjct: 105 TLMEGQEPIARKVVEQGMFVKHCKVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKE 164
Query: 91 VCKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLEVQVDNG 144
+ K+ I EK R+W+ + + PL+ D T+ DA L Q +++E + ++G
Sbjct: 165 IRKIFSIPDEKETRLWNKY-MSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG 218
>pdb|1VJV|A Chain A, Crystal Structure Of Ubiquitin Carboxyl-terminal Hydrolase
6 (yfr010w) From Saccharomyces Cerevisiae At 1.74 A
Resolution
Length = 415
Score = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 747 SYVYDLFAISNHYGGLG-GGHYTAYAK-LIDENRWYHFDDSHVSPVSEGDIKTSAA 800
S VY+L + H G GHY A+ + +DEN+WY F+D VS V + I++ A
Sbjct: 343 SCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAG 398
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 12/108 (11%)
Query: 221 QNLGNTCFMNSALQCLVHTPDLAQYFLGDYSDEINTENPLG----MHGELALAFGDLLRK 276
+N GNTC++N+ LQ L DL L +Y+ N +H ++ +
Sbjct: 28 KNXGNTCYLNATLQALYRVNDLRDXIL-NYNPSQGVSNSGAQDEEIHKQIVIEXKRCFEN 86
Query: 277 LWSSGRAAVAPRAFKGKLARFAPQFSG-------YNQHDSQELLAFLL 317
L + +V P L + PQF+ Y Q D++EL L
Sbjct: 87 LQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLF 134
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 38/132 (28%), Positives = 57/132 (43%), Gaps = 9/132 (6%)
Query: 662 SLFSCLDAFLTEEPLGPDDMWYCPQCKEH--RQATKKLDLWMLPDVLVFHLKRFSYSRYL 719
++F ++ E L D+ + EH ++A K + LP VL L RF Y
Sbjct: 321 NIFESFVDYVAVEQLDGDNKY---DAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQT 377
Query: 720 KN--KLDTFVNFPILNLDLSKYMKSKDGESYV-YDLFAISNHYGGLGGGHYTAYAKLIDE 776
K++ FP L L ++++ D + Y L A+ H G GGHY Y +
Sbjct: 378 DQNIKINDRFEFP-EQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGD 436
Query: 777 NRWYHFDDSHVS 788
+W FDD VS
Sbjct: 437 GKWCKFDDDVVS 448
Score = 36.2 bits (82), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 54/138 (39%), Gaps = 27/138 (19%)
Query: 221 QNLGNTCFMNSALQCLVHTPDL--AQYFLGDYSDEINTENPLGMHGELALAFGDLLRKLW 278
+N G TC+MNS LQ L T L A Y + D+ + PL L++++
Sbjct: 179 KNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLA------------LQRVF 226
Query: 279 SSGRAAVAPRAFKGKLARFAPQ-FSGYNQHDSQELLAFLLDGLHEDLN------------ 325
+ + P K F + + QHD QEL LLD + +
Sbjct: 227 YELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLF 286
Query: 326 RVKQKPYIEMKDSGGRPD 343
R K YI+ K+ R D
Sbjct: 287 RGKMVSYIQCKEVDYRSD 304
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/170 (22%), Positives = 70/170 (41%), Gaps = 18/170 (10%)
Query: 222 NLGNTCFMNSALQCLVHTPDLAQYFLGDYSDEINTENPLGMHGELALAFGDLLRKLWSSG 281
NLGNTC+MN+ +QC+ P+L L Y+ + + + A DL + +
Sbjct: 19 NLGNTCYMNATVQCIRSVPELKDA-LKRYAGALRASGEMASAQYITAALRDLFDSMDKTS 77
Query: 282 RAAVAPRAFKGKLARFAPQFS------GYNQHDSQELLAFLLDGLHEDLNRVKQKPYIEM 335
+++ P L PQF+ Y Q D+ E ++ L + L ++
Sbjct: 78 -SSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIED------ 130
Query: 336 KDSGGRPDEEVANECWKNHKARNDSLIVDVFQGQYKSTLVCPVCSKVSIT 385
DS D A+ ++ SLI F ++++T+ C + +T
Sbjct: 131 -DSVKETDSSSAS---AATPSKKKSLIDQFFGVEFETTMKCTESEEEEVT 176
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 750 YDLFAISNHYG-GLGGGHYTAYAKLIDENRWYHFDDSHVSPVSEGDIKTSA-------AY 801
YDL A+ H G GHY ++ K ++ W FDD VS V+ DI + AY
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKR-KQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAY 386
Query: 802 VLFY--RRVK 809
VL Y RRV+
Sbjct: 387 VLLYGPRRVE 396
>pdb|4A3P|A Chain A, Structure Of Usp15 Dusp-Ubl Deletion Mutant
Length = 217
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 59/114 (51%), Gaps = 5/114 (4%)
Query: 33 SFFVGGPALPRKMISEGIVNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEK-V 91
+ G + RK++ +G+ +VEV+ LKL ++ + + V R KA T EK +
Sbjct: 102 TLMEGQEPIARKVVEQGMFC--KVEVYLTELKLCENGNMNNVVTRRFSKADTIDTIEKEI 159
Query: 92 CKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLEVQVDNG 144
K+ I EK R+W+ + + PL+ D T+ DA L Q +++E + ++G
Sbjct: 160 RKIFSIPDEKETRLWNKY-MSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG 212
>pdb|3JYU|A Chain A, Crystal Structure Of The N-Terminal Domains Of The
Ubiquitin Specific Peptidase 4 (Usp4)
pdb|3JYU|B Chain B, Crystal Structure Of The N-Terminal Domains Of The
Ubiquitin Specific Peptidase 4 (Usp4)
Length = 231
Score = 38.5 bits (88), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 37/134 (27%), Positives = 63/134 (47%), Gaps = 12/134 (8%)
Query: 14 VEIWKKGRTMFWYLSKSGKSFFVGGPALPRKMISEGI-VNEKRVEVFXLCLKLIDSRDNS 72
E W K + WY G+ V RK++ G+ V +VEV+ L LKL ++ D +
Sbjct: 100 AEAWNK--LLNWYGCVEGQQPIV------RKVVEHGLFVKHCKVEVYLLELKLCENSDPT 151
Query: 73 QTV-IRLSKKASTRQLYEKVCKLRGIEQEK-ARIWDYFNKQRSTSPLDVSDQTLDDAMLQ 130
+ SK + + ++ KL I E+ R+W+ + + L D T+ DA L
Sbjct: 152 NVLSCHFSKADTIATIEKEXRKLFNIPAERETRLWNKY-XSNTYEQLSKLDNTIQDAGLY 210
Query: 131 MDQDILLEVQVDNG 144
Q +++E Q ++G
Sbjct: 211 QGQVLVIEPQNEDG 224
>pdb|4B9Y|A Chain A, Crystal Structure Of Apo Agd31b, Alpha-transglucosylase In
Glycoside Hydrolase Family 31
pdb|4B9Z|A Chain A, Crystal Structure Of Agd31b, Alpha-transglucosylase,
Complexed With Acarbose
pdb|4BA0|A Chain A, Crystal Structure Of Agd31b, Alpha-transglucosylase,
Complexed With 5f-alpha-glcf
Length = 817
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 37/130 (28%), Positives = 48/130 (36%), Gaps = 23/130 (17%)
Query: 351 WKNHKARNDSLIVDVFQG----QYKSTLVCPVCSKVSITFDPFMYLTLPLPSTVTRTMTV 406
+K HK RND L++ QG Q+KS V + P L P S + +T
Sbjct: 38 YKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALAQP-ESAIKAQLTE 96
Query: 407 TVFYANGSGLPMPFTVTLMKHGCCKDLILALSTACCLKIDEGLLLAEVYNHQI------F 460
T + SG G I A D LLLAE Q+ F
Sbjct: 97 TENHLQFSG------------GTLTARIQKRPFAISYYRDSELLLAEESGFQVNTDKINF 144
Query: 461 RFFENPAELI 470
RF+ +P E I
Sbjct: 145 RFYLSPGEKI 154
>pdb|3HJE|A Chain A, Crystal Structure Of Sulfolobus Tokodaii Hypothetical
Maltooligosyl Trehalose Synthase
Length = 704
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 719 LKNKLDTFVNFPILNLDLSKYMKSKDGESYVYDLFAISNHYGGLGGGHYTAYAKLIDE 776
++N+LD FV + +L LS +K++ G ++ YD+ + LGG Y +LIDE
Sbjct: 17 IRNRLDYFVELGVTHLYLSPVLKARPGSTHGYDVVDYNTINDELGGEE--EYIRLIDE 72
>pdb|1YN4|A Chain A, Crystal Structures Of Eap Domains From Staphylococcus
Aureus Reveal An Unexpected Homology To Bacterial
Superantigens
Length = 99
Score = 32.3 bits (72), Expect = 0.96, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 33/73 (45%)
Query: 576 NESVETAELEDLCSRELSFQLSLTDERISSCKPIQKDSILKPGKHIKVLLDWTDDVHELY 635
N+ V E++ EL+ Q +T E+I++ + L G V L DD
Sbjct: 27 NKKVLYQEIDSKVKNELASQRGVTTEKINNAQTATYTLTLNDGNKKVVNLKKNDDAKNSI 86
Query: 636 DPSYIKDLPVVHK 648
DPS IK + +V K
Sbjct: 87 DPSTIKQIQIVVK 99
>pdb|2B83|A Chain A, A Single Amino Acid Substitution In The Clostridium
Beijerinckii Alcohol Dehydrogenase Is Critical For
Thermostabilization
pdb|2B83|B Chain B, A Single Amino Acid Substitution In The Clostridium
Beijerinckii Alcohol Dehydrogenase Is Critical For
Thermostabilization
pdb|2B83|C Chain C, A Single Amino Acid Substitution In The Clostridium
Beijerinckii Alcohol Dehydrogenase Is Critical For
Thermostabilization
pdb|2B83|D Chain D, A Single Amino Acid Substitution In The Clostridium
Beijerinckii Alcohol Dehydrogenase Is Critical For
Thermostabilization
Length = 351
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 12/117 (10%)
Query: 91 VCKLRGIEQEK--ARIWDYFNKQRSTSPLDVSDQTLDDAMLQMDQDILLE-------VQV 141
+ KL IE+E+ A +D + + SP T+ + L ++++L V+V
Sbjct: 9 INKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEV 68
Query: 142 DNGISMDSTGNDLALVP-IEPSRSSLTI-AGGPALSNGHTTGYRFNQYPGSSFGSTF 196
+ + D D +VP P SL + AG P SNG G++F+ + FG F
Sbjct: 69 GSEVK-DFKPGDRVIVPCTTPDWRSLEVQAGFPQHSNGMLAGWKFSNFKDGVFGEYF 124
>pdb|3K8Z|A Chain A, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|B Chain B, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|C Chain C, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|D Chain D, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|E Chain E, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
pdb|3K8Z|F Chain F, Crystal Structure Of Gudb1 A Decryptified Secondary
Glutamate Dehydrogenase From B. Subtilis
Length = 423
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%)
Query: 120 SDQTLDDAMLQMDQDILLEVQVDNGISMDSTGNDLALVPIEPSRSSLTIAGGPALSN 176
+D + +L++D DIL+ ++N I+ ++ N A + +E + T+ G LS+
Sbjct: 282 NDTITNQELLELDCDILVPAAIENQITEENAHNIRAKIVVEAANGPTTLEGTKILSD 338
>pdb|1SIJ|A Chain A, Crystal Structure Of The Aldehyde Dehydrogenase (A.K.A.
Aor Or Mop) Of Desulfovibrio Gigas Covalently Bound To
[aso3]-
pdb|1VLB|A Chain A, Structure Refinement Of The Aldehyde Oxidoreductase From
Desulfovibrio Gigas At 1.28 A
pdb|3FAH|A Chain A, Glycerol Inhibited Form Of Aldehyde Oxidoreductase From
Desulfovibrio Gigas
pdb|3FC4|A Chain A, Ethylene Glycol Inhibited Form Of Aldehyde Oxidoreductase
From Desulfovibrio Gigas
pdb|3L4P|A Chain A, Crystal Structure Of The Aldehyde Dehydrogenase (A.K.A.
Aor Or Mop) Of Desulfovibrio Gigas Covalently Bound To
[aso3]-
Length = 907
Score = 29.6 bits (65), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 49/102 (48%), Gaps = 13/102 (12%)
Query: 505 ASDYLKGSERKLFGAPLVTYLEEEHLSGADIDIAVSKL-LSPLRRTYSSAKAHG-----G 558
A++++ GS + +GAP + E +D+ KL + PL Y +A G G
Sbjct: 523 ATNHVWGSAFRGYGAPQSMFASE-----CLMDMLAEKLGMDPLELRYKNAYRPGDTNPTG 577
Query: 559 KENGF--LPEVIDELSNSHNESVETAELEDLCSRELSFQLSL 598
+E LP++ID+L + ++E A+ E + + +S+
Sbjct: 578 QEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISI 619
>pdb|2K8H|A Chain A, Solution Structure Of Sumo From Trypanosoma Brucei
Length = 110
Score = 29.3 bits (64), Expect = 9.3, Method: Composition-based stats.
Identities = 19/92 (20%), Positives = 46/92 (50%), Gaps = 4/92 (4%)
Query: 42 PRKMISEGIVNEKRVEVFXLCLKLIDSRDNSQTVIRLSKKASTRQLYEKVCKLRGIEQEK 101
P EG + E + +K++++ D ++ R+ + + ++L + CK +GI +
Sbjct: 8 PSNNGGEGAEGTCKEETALVAVKVVNA-DGAEMFFRIKSRTALKKLIDTYCKKQGISRNS 66
Query: 102 AR-IWD--YFNKQRSTSPLDVSDQTLDDAMLQ 130
R ++D ++ ++ L + D + DAM++
Sbjct: 67 VRFLFDGTPIDETKTPEELGMEDDDVIDAMVE 98
>pdb|4DGK|A Chain A, Crystal Structure Of Phytoene Desaturase Crti From Pantoea
Ananatis
Length = 501
Score = 29.3 bits (64), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 123 TLDDAMLQMDQDILLEVQVDNGIS-MDSTGNDLALVPIEPSRSSLTIAGGPALSNGHTTG 181
L M+++ QD+ EV ++ +S M++TGN + V +E R LT A HT
Sbjct: 222 ALVQGMIKLFQDLGGEVVLNARVSHMETTGNKIEAVHLEDGRRFLTQAVASNADVVHTYR 281
Query: 182 YRFNQYPGS 190
+Q+P +
Sbjct: 282 DLLSQHPAA 290
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 29.3 bits (64), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 21/44 (47%)
Query: 233 LQCLVHTPDLAQYFLGDYSDEINTENPLGMHGELALAFGDLLRK 276
LQ L T + Y+L D DE+ P G EL + G LL K
Sbjct: 78 LQLLAGTYKIVGYYLYDGLDEVLLAGPAGDDNELTVVSGGLLEK 121
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 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,340,589
Number of Sequences: 62578
Number of extensions: 1092583
Number of successful extensions: 2517
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 2427
Number of HSP's gapped (non-prelim): 69
length of query: 825
length of database: 14,973,337
effective HSP length: 107
effective length of query: 718
effective length of database: 8,277,491
effective search space: 5943238538
effective search space used: 5943238538
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: 56 (26.2 bits)