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= psy2295
(276 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 73/220 (33%), Positives = 108/220 (49%), Gaps = 25/220 (11%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
++GLKN GATCY+NSLLQ F RKAV D K+ P
Sbjct: 175 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLA------------- 221
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTLG---LDRSYQQDAQEFSKLFLSNFVEEKFRVQSL 177
LQ +F +QHS+K V + G LD Q D QE ++ L N VE K +
Sbjct: 222 -LQRVFYELQHSDK-PVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN-VENKMKGTC- 277
Query: 178 PHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNV--CKTLDESMREFLKEELL 235
++ I F G+ V +C +DR E +Y++ +++ K + ES +++ E L
Sbjct: 278 --VEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQL 335
Query: 236 EGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFD 275
+GD++Y G Q A + ++ LP VL+LQLMRF++D
Sbjct: 336 DGDNKYDAGEHG-LQEAEKGVKFLTLPPVLHLQLMRFMYD 374
>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 = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 73/220 (33%), Positives = 108/220 (49%), Gaps = 25/220 (11%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
++GLKN GATCY+NSLLQ F RKAV D K+ P
Sbjct: 6 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLA------------- 52
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTLG---LDRSYQQDAQEFSKLFLSNFVEEKFRVQSL 177
LQ +F +QHS+K V + G LD Q D QE ++ L N VE K +
Sbjct: 53 -LQRVFYELQHSDK-PVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN-VENKMKGTC- 108
Query: 178 PHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNV--CKTLDESMREFLKEELL 235
++ I F G+ V +C +DR E +Y++ +++ K + ES +++ E L
Sbjct: 109 --VEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQL 166
Query: 236 EGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFD 275
+GD++Y G Q A + ++ LP VL+LQLMRF++D
Sbjct: 167 DGDNKYDAGEHG-LQEAEKGVKFLTLPPVLHLQLMRFMYD 205
>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 = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 72/220 (32%), Positives = 105/220 (47%), Gaps = 25/220 (11%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
++GLKN GATCY NSLLQ F RKAV D K+ P
Sbjct: 6 YVGLKNQGATCYXNSLLQTLFFTNQLRKAVYXXPTEGDDSSKSVPLA------------- 52
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTLG---LDRSYQQDAQEFSKLFLSNFVEEKFRVQSL 177
LQ +F +QHS+K V + G LD Q D QE ++ L N VE K +
Sbjct: 53 -LQRVFYELQHSDK-PVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDN-VENKXKGTC- 108
Query: 178 PHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNV--CKTLDESMREFLKEELL 235
++ I F G+ V +C +DR E +Y++ +++ K + ES +++ E L
Sbjct: 109 --VEGTIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQL 166
Query: 236 EGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFD 275
+GD++Y G Q A + ++ LP VL+LQL RF +D
Sbjct: 167 DGDNKYDAGEHG-LQEAEKGVKFLTLPPVLHLQLXRFXYD 205
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 71.2 bits (173), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 64/250 (25%), Positives = 111/250 (44%), Gaps = 43/250 (17%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG TCY+NS+LQ N P + N +D ++N LG G + I
Sbjct: 62 LTGLRNLGNTCYMNSILQC-LCNAPHLADYFNRNCYQDDINRSN-LLGHKGEVAEEFGI- 118
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEE----- 170
+ + + P DF +T+G QQD+QE LFL + + E
Sbjct: 119 ----IMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELL-LFLMDGLHEDLNKA 173
Query: 171 ----KFRVQSLPHIKNF-----------------IKDYFSGEYVYVTKCFACGNETDRSE 209
+++ ++ H+ +F I F G++ +C C ++ E
Sbjct: 174 DNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFE 233
Query: 210 IFYELVVNVCKT----LDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVL 265
F L + + T L + +R F KEE L +++++C+ C ++++ ++I + LP VL
Sbjct: 234 AFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVL 293
Query: 266 NLQLMRFVFD 275
+ L RF +D
Sbjct: 294 LVHLKRFSYD 303
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 70.9 bits (172), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 66/250 (26%), Positives = 111/250 (44%), Gaps = 43/250 (17%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG TCY NS+LQ N P + N +D ++N LG G E G
Sbjct: 62 LTGLRNLGNTCYXNSILQC-LCNAPHLADYFNRNCYQDDINRSN-LLGHKG--EVAEEFG 117
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEE----- 170
+ Q+ + P DF +T+G QQD+QE LFL + + E
Sbjct: 118 IIXKALWTGQYR---YISPKDFKITIGKINDQFAGYSQQDSQELL-LFLXDGLHEDLNKA 173
Query: 171 ----KFRVQSLPHIKNF-----------------IKDYFSGEYVYVTKCFACGNETDRSE 209
+++ ++ H+ +F I F G++ +C C ++ E
Sbjct: 174 DNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFE 233
Query: 210 IFYELVVNVCKT----LDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVL 265
F L + + T L + +R F KEE L +++++C+ C ++++ ++I + LP VL
Sbjct: 234 AFXYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVL 293
Query: 266 NLQLMRFVFD 275
+ L RF +D
Sbjct: 294 LVHLKRFSYD 303
>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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 70/284 (24%), Positives = 107/284 (37%), Gaps = 62/284 (21%)
Query: 46 SDDFDPDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNP 105
SDD L + +GL+NLG TC++N++LQ P R L + R++
Sbjct: 1 SDDKMAHHTLLLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRA 60
Query: 106 SLGFSGFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTL-----GLDRSYQQDAQEFS 160
F + A+ H A V+PT F QQDAQEF
Sbjct: 61 QELTEAFADVIGALWHPDSCEA---------VNPTRFRAVFQKYVPSFSGYSQQDAQEFL 111
Query: 161 KLFLSNF-VEEKFRVQSLPHI--------------------------------------- 180
KL + +E R + P I
Sbjct: 112 KLLMERLHLEINRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLERE 171
Query: 181 KNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNVCK--------TLDESMREFLKE 232
+ I D F G+ KC ACG + E+F +L + + K +L + F KE
Sbjct: 172 DSKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKE 231
Query: 233 ELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFDR 276
E LE ++ C+RC +K + +++ ++ P++L L L RF R
Sbjct: 232 EELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASR 275
>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 = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 66/274 (24%), Positives = 105/274 (38%), Gaps = 62/274 (22%)
Query: 56 RDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEP 115
R + +GL+NLG TC++N++LQ P R L + R++ G
Sbjct: 17 RGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVP---------GGGRAQ 67
Query: 116 QTAIGHLQMLFALMQHSNKLLVDPTDFVLTL-----GLDRSYQQDAQEFSKLFLSNF-VE 169
+ ++ AL + V+PT F QQDAQEF KL + +E
Sbjct: 68 ELTEAFADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLE 127
Query: 170 EKFRVQSLPHI---------------------------------------KNFIKDYFSG 190
R + P I + I D F G
Sbjct: 128 INRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVG 187
Query: 191 EYVYVTKCFACGNETDRSEIFYELVVNVCK--------TLDESMREFLKEELLEGDDQYF 242
+ KC ACG + E+F +L + + K +L + F KEE LE ++
Sbjct: 188 QLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPV 247
Query: 243 CNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFDR 276
C+RC +K + +++ ++ P++L L L RF R
Sbjct: 248 CDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASR 281
>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 = 65.5 bits (158), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 65/268 (24%), Positives = 103/268 (38%), Gaps = 62/268 (23%)
Query: 62 IGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGH 121
+GL+NLG TC++N++LQ P R L + R++ G +
Sbjct: 4 VGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVP---------GGGRAQELTEAF 54
Query: 122 LQMLFALMQHSNKLLVDPTDFVLTL-----GLDRSYQQDAQEFSKLFLSNF-VEEKFRVQ 175
++ AL + V+PT F QQDAQEF KL + +E R +
Sbjct: 55 ADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGR 114
Query: 176 SLPHI---------------------------------------KNFIKDYFSGEYVYVT 196
P I + I D F G+
Sbjct: 115 RAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCL 174
Query: 197 KCFACGNETDRSEIFYELVVNVCK--------TLDESMREFLKEELLEGDDQYFCNRCGK 248
KC ACG + E+F +L + + K +L + F KEE LE ++ C+RC +
Sbjct: 175 KCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQ 234
Query: 249 KQNAGRRIRLKYLPKVLNLQLMRFVFDR 276
K + +++ ++ P++L L L RF R
Sbjct: 235 KTRSTKKLTVQRFPRILVLHLNRFSASR 262
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 65/244 (26%), Positives = 104/244 (42%), Gaps = 28/244 (11%)
Query: 51 PDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFS 110
P E RD GL N+G+TC+++S+LQ HN F + + + + ++ P FS
Sbjct: 133 PSMERRDG--LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRS-PDKCFS 189
Query: 111 GFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKL 162
+ + + S+ T F+ L L QQDA EF +
Sbjct: 190 CALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ- 248
Query: 163 FLSNFVEEKFRVQSLPHIKN-----------FIKDYFSGEYVYVTKCFACGNETDRS-EI 210
F+ N + + + V LP+ K + F G C C N + + +
Sbjct: 249 FIINQIHQSY-VLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDP 307
Query: 211 FYELVVNVC--KTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQ 268
F +L +++ K L E + F K+E L+ D Y C C Q+A +++ + LP VL LQ
Sbjct: 308 FLDLSLDIKDKKKLYECLDSFHKKEQLK-DFNYHCGECNSTQDAIKQLGIHKLPSVLVLQ 366
Query: 269 LMRF 272
L RF
Sbjct: 367 LKRF 370
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 65/244 (26%), Positives = 104/244 (42%), Gaps = 28/244 (11%)
Query: 51 PDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFS 110
P E RD GL N+G+TC+++S+LQ HN F + + + + ++ P FS
Sbjct: 128 PSMERRDG--LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRS-PDKCFS 184
Query: 111 GFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKL 162
+ + + S+ T F+ L L QQDA EF +
Sbjct: 185 CALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ- 243
Query: 163 FLSNFVEEKFRVQSLPHIKN-----------FIKDYFSGEYVYVTKCFACGNETDRS-EI 210
F+ N + + + V LP+ K + F G C C N + + +
Sbjct: 244 FIINQIHQSY-VLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDP 302
Query: 211 FYELVVNVC--KTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQ 268
F +L +++ K L E + F K+E L+ D Y C C Q+A +++ + LP VL LQ
Sbjct: 303 FLDLSLDIKDKKKLYECLDSFHKKEQLK-DFNYHCGECNSTQDAIKQLGIHKLPSVLVLQ 361
Query: 269 LMRF 272
L RF
Sbjct: 362 LKRF 365
>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 = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 65/244 (26%), Positives = 103/244 (42%), Gaps = 28/244 (11%)
Query: 51 PDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFS 110
P E RD GL N+G TC+++S+LQ HN F + + + + ++ P FS
Sbjct: 133 PSMERRDG--LSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRS-PDKCFS 189
Query: 111 GFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKL 162
+ + + S+ T F+ L L QQDA EF +
Sbjct: 190 CALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ- 248
Query: 163 FLSNFVEEKFRVQSLPHIKN-----------FIKDYFSGEYVYVTKCFACGNETDRS-EI 210
F+ N + + + V LP+ K + F G C C N + + +
Sbjct: 249 FIINQIHQSY-VLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDP 307
Query: 211 FYELVVNVC--KTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQ 268
F +L +++ K L E + F K+E L+ D Y C C Q+A +++ + LP VL LQ
Sbjct: 308 FLDLSLDIKDKKKLYECLDSFHKKEQLK-DFNYHCGECNSTQDAIKQLGIHKLPSVLVLQ 366
Query: 269 LMRF 272
L RF
Sbjct: 367 LKRF 370
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 64/255 (25%), Positives = 105/255 (41%), Gaps = 50/255 (19%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG TC++NS+LQ + R L D +N +
Sbjct: 9 LAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFA------ 62
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKLFLSNFVEEKF 172
+++ + S +V P++F + G + QQDAQEF + L E
Sbjct: 63 --KLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYN---QQDAQEFLRFLLDGLHNEVN 117
Query: 173 RV--------QSLPHIKN-----------------FIKDYFSGEYVYVTKCFACGNETDR 207
RV ++L H+ + I D F G+ C CG +
Sbjct: 118 RVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTV 177
Query: 208 SEIFYELVVNVCK------TLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYL 261
+ F++L + + K TL + MR F KE++L+GD++ C RC ++ ++ ++
Sbjct: 178 FDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRF 237
Query: 262 PKVLNLQLMRFVFDR 276
PK+L L L RF R
Sbjct: 238 PKILVLHLKRFSESR 252
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 64/255 (25%), Positives = 105/255 (41%), Gaps = 50/255 (19%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG TC++NS+LQ + R L D +N +
Sbjct: 28 LAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFA------ 81
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKLFLSNFVEEKF 172
+++ + S +V P++F + G + QQDAQEF + L E
Sbjct: 82 --KLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYN---QQDAQEFLRFLLDGLHNEVN 136
Query: 173 RV--------QSLPHIKN-----------------FIKDYFSGEYVYVTKCFACGNETDR 207
RV ++L H+ + I D F G+ C CG +
Sbjct: 137 RVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTV 196
Query: 208 SEIFYELVVNVCK------TLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYL 261
+ F++L + + K TL + MR F KE++L+GD++ C RC ++ ++ ++
Sbjct: 197 FDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRF 256
Query: 262 PKVLNLQLMRFVFDR 276
PK+L L L RF R
Sbjct: 257 PKILVLHLKRFSESR 271
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 64/255 (25%), Positives = 103/255 (40%), Gaps = 50/255 (19%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG TC++NS+LQ + R L D +N +
Sbjct: 35 LAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFA------ 88
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKLFLSNFVEEKF 172
+++ + S +V P++F + G + QQDAQEF + L E
Sbjct: 89 --KLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYN---QQDAQEFLRFLLDGLHNEVN 143
Query: 173 RV--------QSLPHIKN-----------------FIKDYFSGEYVYVTKCFACGNETDR 207
RV ++L H+ + I D F G+ C CG +
Sbjct: 144 RVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTV 203
Query: 208 SEIFYELVVNVCK------TLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYL 261
+ F++L + + K TL + MR F KE++L+GD C RC ++ ++ ++
Sbjct: 204 FDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRF 263
Query: 262 PKVLNLQLMRFVFDR 276
PK+L L L RF R
Sbjct: 264 PKILVLHLKRFSESR 278
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 63/255 (24%), Positives = 104/255 (40%), Gaps = 50/255 (19%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIG 120
GL+NLG T ++NS+LQ + R L D +N +
Sbjct: 9 LAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFA------ 62
Query: 121 HLQMLFALMQHSNKLLVDPTDFVLTL--------GLDRSYQQDAQEFSKLFLSNFVEEKF 172
+++ + S +V P++F + G + QQDAQEF + L E
Sbjct: 63 --KLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYN---QQDAQEFLRFLLDGLHNEVN 117
Query: 173 RV--------QSLPHIKN-----------------FIKDYFSGEYVYVTKCFACGNETDR 207
RV ++L H+ + I D F G+ C CG +
Sbjct: 118 RVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTV 177
Query: 208 SEIFYELVVNVCK------TLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYL 261
+ F++L + + K TL + MR F KE++L+GD++ C RC ++ ++ ++
Sbjct: 178 FDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRF 237
Query: 262 PKVLNLQLMRFVFDR 276
PK+L L L RF R
Sbjct: 238 PKILVLHLKRFSESR 252
>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 = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 63/265 (23%), Positives = 93/265 (35%), Gaps = 58/265 (21%)
Query: 63 GLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGHL 122
GL NLG T ++NS LQ + P L + E ++NP LG G + A +
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLK-DEYEAEINRDNP-LGMKG----EIAEAYA 63
Query: 123 QMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEEKFRVQSL 177
+ L M V P F +G QQD+QE L E+ RV+
Sbjct: 64 E-LIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKK 122
Query: 178 PHIK-------------------------NFIKDYFSGEYVYVTKCFACGNETDRSEIFY 212
P+++ + I D F G + C C + + F
Sbjct: 123 PYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFC 182
Query: 213 ELVVNVCKTLDESMRE---------------------FLKEELLEGDDQYFCNRCGKKQN 251
L + + D M F E L D ++C C K Q
Sbjct: 183 YLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQ 242
Query: 252 AGRRIRLKYLPKVLNLQLMRFVFDR 276
A ++ L LPK+L + L RF ++R
Sbjct: 243 ATKKFDLWSLPKILVVHLKRFSYNR 267
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 68/257 (26%), Positives = 107/257 (41%), Gaps = 63/257 (24%)
Query: 51 PDQELRDPNEF-IGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGF 109
P+Q+++ + +G KN G TCY+N+ LQ + R +L++ NPS G
Sbjct: 13 PEQQVQQFAQLPVGFKNXGNTCYLNATLQALYRVNDLRDXILNY----------NPSQGV 62
Query: 110 SGFYEPQTAIGHLQML------FALMQHSNKLLVDPTDFVLTLGLDRSY----------- 152
S I H Q++ F +Q+ + V P VL L + Y
Sbjct: 63 SNSGAQDEEI-HKQIVIEXKRCFENLQNKSFKSVLPV--VLLNTLRKCYPQFAERDSQGG 119
Query: 153 ---QQDAQE-FSKLFLSNFV------EEKFRVQSLPHIKNFIKDYFSGEYVYVTKCFACG 202
QQDA+E F++LF S + E FR+Q K IKD + + V +
Sbjct: 120 FYKQQDAEELFTQLFHSXSIVFGDKFSEDFRIQ----FKTTIKDTANDNDITVKE----- 170
Query: 203 NETDRSEIFYELVVNVCKTLDESMREFLKEELLEGDDQYFCNR---CGKKQNAGRRIRLK 259
NE+D +L ++ T + F + LLEG ++ R G ++
Sbjct: 171 NESDS-----KLQCHISGTTN-----FXRNGLLEGLNEKIEKRSDLTGANSIYSVEKKIS 220
Query: 260 YLPKVLNLQLMRFVFDR 276
LPK L +Q +RF + R
Sbjct: 221 RLPKFLTVQYVRFFWKR 237
>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 = 0.019, Method: Composition-based stats.
Identities = 37/139 (26%), Positives = 58/139 (41%), Gaps = 25/139 (17%)
Query: 61 FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGF----------- 109
+ G++NLG +CY+NS++Q+ F F++ +D + +P+ F
Sbjct: 344 YTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGL 403
Query: 110 -SGFYE---PQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFS 160
SG Y P++ G Q + + P F +G + QQDAQEF
Sbjct: 404 LSGEYSKPVPESGDGER----VPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFF 459
Query: 161 KLFLSNFVEEKFRVQSLPH 179
L L N VE R P+
Sbjct: 460 -LHLINMVERNCRSSENPN 477
>pdb|1LW7|A Chain A, Nadr Protein From Haemophilus Influenzae
Length = 365
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 115 PQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLGLDRSYQQDAQEF 159
PQ A+GH + + ++HS+K+ TDF+ T Y+ A F
Sbjct: 224 PQXALGHQRYIDYAVRHSHKIAFIDTDFITTQAFCIQYEGKAHPF 268
>pdb|3II1|A Chain A, Structural Characterization Of Difunctional Glucanase-
Xylanse Celm2
Length = 535
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 161 KLFLSNFVEEKF---RVQSLPHIKNFIKDYFSGEYVYVTK 197
L+ N+++E + +VQ +P +KN++ Y+ G +T+
Sbjct: 339 SLWDPNYIDETWINDKVQLIPRLKNWVSTYYPGTLTAITE 378
>pdb|3FW6|A Chain A, Crystal Structure Of Celm2, A Bifunctional Glucanase-
Xylanase Protein From A Metagenome Library
Length = 534
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 161 KLFLSNFVEEKF---RVQSLPHIKNFIKDYFSGEYVYVTK 197
L+ N+++E + +VQ +P +KN++ Y+ G +T+
Sbjct: 339 SLWDPNYIDETWINDKVQLIPRLKNWVSTYYPGTLTAITE 378
>pdb|3IQC|A Chain A, Crystal Structure Of Flis From H. Pylori
pdb|3IQC|B Chain B, Crystal Structure Of Flis From H. Pylori
pdb|3K1I|A Chain A, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
pdb|3K1I|B Chain B, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
Length = 131
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 187 YFSGEYVYVTKCFACGN-ETDRSEIFYELVVNVCKTLDESMREFLKEEL 234
Y +G Y + K N E D S+I +LV+NV + L E+ RE +EL
Sbjct: 84 YLTGLYTHQIKVLTQANVENDASKI--DLVLNVARGLLEAWREIHSDEL 130
>pdb|2DD4|A Chain A, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Recombinant Apo-Enzyme
pdb|2DD4|D Chain D, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Recombinant Apo-Enzyme
pdb|2DD4|G Chain G, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Recombinant Apo-Enzyme
pdb|2DD4|J Chain J, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Recombinant Apo-Enzyme
pdb|2DD5|A Chain A, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Native Holo-Enzyme
pdb|2DD5|D Chain D, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Native Holo-Enzyme
pdb|2DD5|G Chain G, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Native Holo-Enzyme
pdb|2DD5|J Chain J, Thiocyanate Hydrolase (Scnase) From Thiobacillus Thioparus
Native Holo-Enzyme
pdb|2DXB|A Chain A, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|D Chain D, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|G Chain G, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|J Chain J, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|M Chain M, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|P Chain P, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|S Chain S, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXB|V Chain V, Recombinant Thiocyanate Hydrolase Comprising
Partially-Modified Cobalt Centers
pdb|2DXC|A Chain A, Recombinant Thiocyanate Hydrolase, Fully-Matured Form
pdb|2DXC|D Chain D, Recombinant Thiocyanate Hydrolase, Fully-Matured Form
pdb|2DXC|G Chain G, Recombinant Thiocyanate Hydrolase, Fully-Matured Form
pdb|2DXC|J Chain J, Recombinant Thiocyanate Hydrolase, Fully-Matured Form
pdb|2ZZD|A Chain A, Recombinant Thiocyanate Hydrolase, Air-Oxidized Form Of
Holo-Enzyme
pdb|2ZZD|D Chain D, Recombinant Thiocyanate Hydrolase, Air-Oxidized Form Of
Holo-Enzyme
pdb|2ZZD|G Chain G, Recombinant Thiocyanate Hydrolase, Air-Oxidized Form Of
Holo-Enzyme
pdb|2ZZD|J Chain J, Recombinant Thiocyanate Hydrolase, Air-Oxidized Form Of
Holo-Enzyme
Length = 126
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 237 GDDQYFCNRCGKKQ-NAGRRIRLKYLPKVLNLQLMRFV 273
GD Q F GK + N G R+R+K LP + + M +
Sbjct: 23 GDPQCFKGMAGKSKFNVGDRVRIKDLPDLFYTRTMTYT 60
>pdb|3UA4|A Chain A, Crystal Structure Of Protein Arginine Methyltransferase
Prmt5
pdb|3UA4|B Chain B, Crystal Structure Of Protein Arginine Methyltransferase
Prmt5
Length = 745
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 111 GFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLGLDRSYQQDAQEFSKLFLSNFVEE 170
GF +P + L F + S + L T F+ + S Q + K +S + +
Sbjct: 492 GFEQPDIIVSELLGSFGDNELSPECLDGVTGFLKPTTI--SIPQKYTSYVKPIMSTHIHQ 549
Query: 171 KFRVQSLPHIKNFIKDYFSGE 191
+ QS+P++ I + GE
Sbjct: 550 TIKAQSIPYLSRAIPSHGRGE 570
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
0.324 0.141 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,528,124
Number of Sequences: 62578
Number of extensions: 365711
Number of successful extensions: 795
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 746
Number of HSP's gapped (non-prelim): 32
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)