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= psy7711
(577 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 374 bits (960), Expect = e-104, Method: Compositional matrix adjust.
Identities = 199/400 (49%), Positives = 254/400 (63%), Gaps = 46/400 (11%)
Query: 189 LPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSN--PAQSITASLRDLYEC 246
LP GL NLGNTCYMNA +QC+++VPEL+ ALK G L+ AQ ITA+LRDL++
Sbjct: 13 LPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDS 72
Query: 247 MDNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPG-EN 305
MD K S SI P I+LQ LH FP+FA+K + G Y+QQDANECW +M+R+L+ L E+
Sbjct: 73 MD--KTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIED 130
Query: 306 EEGQD-----------SAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYIT 354
+ ++ S K S I+Q+F +T +KC+ESE E TKG E+ QLSC+I
Sbjct: 131 DSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFIN 190
Query: 355 TDVKYMLPGLKNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERIN 414
+VKY+ GLK +LQ++ITK+SP+L R+A+Y+K+SK+SRLPAYLTIQ VRFFYKEKE +N
Sbjct: 191 QEVKYLFTGLKLRLQEEITKQSPTLQRNALYIKSSKISRLPAYLTIQMVRFFYKEKESVN 250
Query: 415 AKVLKDIKFPIEFDAYELCTPELQAKLAPMRXXXXXXXXXXXXXXXRTQYVFISIPMDEI 474
AKVLKD+KFP+ D YELCTPELQ K+ R T S P E+
Sbjct: 251 AKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDK-KSSPQKEV 309
Query: 475 YVRFGQKIYAPVGDRIQDFGVKSTEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRT 534
Y P F DIGSNN GYY LQAVLTH+GR+
Sbjct: 310 K-------YEP-------FSFAD---------------DIGSNNCGYYDLQAVLTHQGRS 340
Query: 535 SSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLKLSGGG 574
SSSGHYV+WVK+ WIK DDDKV ++ E++L+LSGGG
Sbjct: 341 SSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGG 380
Score = 98.6 bits (244), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 48/89 (53%), Positives = 62/89 (69%), Gaps = 4/89 (4%)
Query: 99 DMNESERAVSLDLPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSN--PAQ 156
DM E + A +++LP GL NLGNTCYMNA +QC+++VPEL+ ALK G L+ AQ
Sbjct: 1 DMTEEQLASAMELPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQ 60
Query: 157 SITASLRDLYECMDNMKISPSISPFIMLQ 185
ITA+LRDL++ MD K S SI P I+LQ
Sbjct: 61 YITAALRDLFDSMD--KTSSSIPPIILLQ 87
>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 = 133 bits (334), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 83/271 (30%), Positives = 130/271 (47%), Gaps = 34/271 (12%)
Query: 189 LPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITAS--------- 239
LP G N GNTCY+NA +Q L V +LR + N NP+Q ++ S
Sbjct: 23 LPVGFKNXGNTCYLNATLQALYRVNDLRDXILNY--------NPSQGVSNSGAQDEEIHK 74
Query: 240 --LRDLYECMDNM--KISPSISPFIMLQVLHNVFPRFADKTDDGS-YMQQDANECWTEMV 294
+ + C +N+ K S+ P ++L L +P+FA++ G Y QQDA E +T++
Sbjct: 75 QIVIEXKRCFENLQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLF 134
Query: 295 RMLKTALPGENEEGQDSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYIT 354
D F Q+ TI DT ++ + K ES +L C+I+
Sbjct: 135 HSXSIVFG-------DKFSEDFRIQFKTTIKDTA-----NDNDITVKENESDSKLQCHIS 182
Query: 355 TDVKYMLPGLKNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERIN 414
+ GL L ++I KRS +++Y K+SRLP +LT+Q+VRFF+K
Sbjct: 183 GTTNFXRNGLLEGLNEKIEKRSDLTGANSIYSVEKKISRLPKFLTVQYVRFFWKRSTNKK 242
Query: 415 AKVLKDIKFPIEFDAYELCTPELQAKLAPMR 445
+K+L+ + FP + D + TPE A+ +R
Sbjct: 243 SKILRKVVFPFQLDVADXLTPEYAAEKVKVR 273
Score = 55.8 bits (133), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 509 PGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP--NGTWIKCDDDKVYPISEEE 566
P ++ G N S Y L V+TH+G S SGHY A+++ W K +DDKV + +E+
Sbjct: 333 PPNLEKGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEK 392
Query: 567 VLKLSGGGK 575
+ L+GGG+
Sbjct: 393 IESLAGGGE 401
>pdb|1WGG|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like
Domain Of Mouse Ubiquitin Specific Protease 14 (Usp14)
Length = 96
Score = 76.6 bits (187), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 39/71 (54%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 14 VKVKWGKXX-XXXXXXXXXXPMLFKAQLYELTGVQIDRQKVMCKGATLKNDEWDNFKLSN 72
V VKWGK PM+FKAQL+ LTGVQ RQKVM KG TLK+D+W N K+ N
Sbjct: 10 VTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDDDWGNIKMKN 69
Query: 73 GSMVLLMGSKE 83
G VL+MGS +
Sbjct: 70 GMTVLMMGSAD 80
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 248
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 249 NMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGE 304
+ +SP + PRF Y QQDA E +R L L E
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFV------GYNQQDAQ----EFLRFLLDGLHNE 115
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 170
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 171 NMKISPSISP--FIMLQGRYLP 190
+ +SP F RY P
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAP 91
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEV 567
+ N Y L AV H G T+ GHY A+ + P G W +D V P+S +V
Sbjct: 278 NTNHAVYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 329
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 248
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 29 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 88
Query: 249 NMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGE 304
+ +SP + PRF Y QQDA E +R L L E
Sbjct: 89 TSSPNDVVSPSEFKTQIQRYAPRFV------GYNQQDAQ----EFLRFLLDGLHNE 134
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 170
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 29 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 88
Query: 171 NMKISPSISP--FIMLQGRYLP 190
+ +SP F RY P
Sbjct: 89 TSSPNDVVSPSEFKTQIQRYAP 110
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEV 567
+ N Y L AV H G T+ GHY A+ + P G W +D V P+S +V
Sbjct: 297 NTNHAVYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 348
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 52/116 (44%), Gaps = 12/116 (10%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 248
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 36 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 95
Query: 249 NMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGE 304
+ +SP + PRF Y QQDA E +R L L E
Sbjct: 96 TSSPNDVVSPSEFKTQIQRYAPRFV------GYNQQDAQ----EFLRFLLDGLHNE 141
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 170
AGL NLGNTC+MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 36 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 95
Query: 171 NMKISPSISP--FIMLQGRYLP 190
+ +SP F RY P
Sbjct: 96 TSSPNDVVSPSEFKTQIQRYAP 117
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEV 567
+ N Y L AV H G T+ GHY A+ + P G W +D V P+S +V
Sbjct: 304 NTNHAVYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 355
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANE 288
+++P V P F+ Y QQDA E
Sbjct: 65 DSCEAVNPTRFRAVFQKYVPSFS------GYSQQDAQE 96
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 172
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 173 KISPSISP--FIMLQGRYLPA 191
+++P F + +Y+P+
Sbjct: 65 DSCEAVNPTRFRAVFQKYVPS 85
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 83
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANE 288
+++P V P F+ Y QQDA E
Sbjct: 84 DSCEAVNPTRFRAVFQKYVPSFS------GYSQQDAQE 115
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 172
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 83
Query: 173 KISPSISP--FIMLQGRYLPA 191
+++P F + +Y+P+
Sbjct: 84 DSCEAVNPTRFRAVFQKYVPS 104
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 77
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANE 288
+++P V P F+ Y QQDA E
Sbjct: 78 DSCEAVNPTRFRAVFQKYVPSFS------GYSQQDAQE 109
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPELRK-ALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 172
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 77
Query: 173 KISPSISP--FIMLQGRYLPA 191
+++P F + +Y+P+
Sbjct: 78 DSCEAVNPTRFRAVFQKYVPS 98
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 38/116 (32%), Positives = 51/116 (43%), Gaps = 12/116 (10%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 248
AGL NLGNT +MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 10 AGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 249 NMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGE 304
+ +SP + PRF Y QQDA E +R L L E
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFV------GYNQQDAQ----EFLRFLLDGLHNE 115
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 38/126 (30%), Positives = 56/126 (44%), Gaps = 14/126 (11%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRK-ALKNL-KGGLQPGSNPAQSITASLRDLYECMD 170
AGL NLGNT +MN+++QCL ELR L+ L L GSN ++ L + +
Sbjct: 10 AGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 171 NMKISPSISP--FIMLQGRYLP--AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGL 226
+ +SP F RY P G N ++ ++ L E+ + L
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHN--EVNRV------TL 121
Query: 227 QPGSNP 232
+P SNP
Sbjct: 122 RPKSNP 127
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEV 567
+ N Y L AV H G T+ GHY A+ + P G W +D V P+S +V
Sbjct: 278 NTNHAVYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 329
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 62/299 (20%), Positives = 118/299 (39%), Gaps = 69/299 (23%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPEL-RKALKNLKGGLQPG-SNPAQSITASLRDLYECM-- 247
G+ NLGN+CY+N+V+Q L ++P+ RK + L+ Q ++P Q + + L +
Sbjct: 346 GIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLS 405
Query: 248 -----------------DNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECW 290
+ ++ I+P + ++ P F+ + QQDA E +
Sbjct: 406 GEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFS------TNRQQDAQEFF 459
Query: 291 TEMVRMLKTALPGENEEGQDSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLS 350
++ M++ ++ S + F +++ ++KC +E T+ + QL
Sbjct: 460 LHLINMVE----------RNCRSSENPNEVFRFLVEEKIKCLATEKVKYTQRVDYIMQLP 509
Query: 351 CYI------------------TTDVKYMLPGLKNK------------LQDQITK-RSPSL 379
+ + K LP L +Q+ S +L
Sbjct: 510 VPMDAALNKEELLEYEEKKRQAEEEKMALPELVRAQVPFSSCLEAYGAPEQVDDFWSTAL 569
Query: 380 DRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIEFDAYELCTPELQ 438
+V VKT++ + P YL IQ +F + + + K+ I+ P E D +L LQ
Sbjct: 570 QAKSVAVKTTRFASFPDYLVIQIKKFTFG-LDWVPKKLDVSIEMPEELDISQLRGTGLQ 627
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPEL-RKALKNLKGGLQPG-SNPAQSITASLRDL 165
G+ NLGN+CY+N+V+Q L ++P+ RK + L+ Q ++P Q + + L
Sbjct: 346 GIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKL 399
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 517 NNSGYYTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKV 559
+ G Y L A ++H G ++ GHYV +KK G W+ +D KV
Sbjct: 792 DGPGKYQLFAFISHMGTSTMCGHYVCHIKK-EGRWVIYNDQKV 833
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLK 569
Y L +++HKG T + GHY+A+ K G W K +D V IS+EEVLK
Sbjct: 416 YELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 462
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 60/272 (22%), Positives = 113/272 (41%), Gaps = 31/272 (11%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RDLYE 245
+GL N+GNTC+M++++QCL P +R ++ + +P + + +L +LY
Sbjct: 142 SGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 201
Query: 246 CMDNMKISPSISP------FIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKT 299
++ + S S + FI L + + + Y QQDA+E W ++ +
Sbjct: 202 ALNTKQASSSSTSTNRQTGFIYL-----LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 256
Query: 300 A----LPGENEEGQDSAK--SSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYI 353
+ LP E + + K + F +++ + C + T + F LS I
Sbjct: 257 SYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTT-IDPFLDLSLDI 315
Query: 354 TTDVKYMLPGL-----KNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYK 408
D K + L K +L+D + +K + +LP+ L +Q RF +
Sbjct: 316 -KDKKKLYECLDSFHKKEQLKD-FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHL 373
Query: 409 EKERINAKVLKDIKFPIEFDAYELCTPELQAK 440
N K+ I+FP + C+ + + K
Sbjct: 374 LNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDK 404
Score = 35.4 bits (80), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 110 DLPAGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RD 164
D +GL N+GNTC+M++++QCL P +R ++ + +P + + +L +
Sbjct: 139 DGLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHE 198
Query: 165 LYECMDNMKISPS 177
LY ++ + S S
Sbjct: 199 LYGALNTKQASSS 211
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLK 569
Y L +++HKG T + GHY+A+ K G W K +D V IS+EEVLK
Sbjct: 411 YELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 457
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 59/272 (21%), Positives = 113/272 (41%), Gaps = 31/272 (11%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RDLYE 245
+GL N+G+TC+M++++QCL P +R ++ + +P + + +L +LY
Sbjct: 137 SGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 196
Query: 246 CMDNMKISPSISP------FIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKT 299
++ + S S + FI L + + + Y QQDA+E W ++ +
Sbjct: 197 ALNTKQASSSSTSTNRQTGFIYL-----LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 251
Query: 300 A----LPGENEEGQDSAK--SSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYI 353
+ LP E + + K + F +++ + C + T + F LS I
Sbjct: 252 SYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTT-IDPFLDLSLDI 310
Query: 354 TTDVKYMLPGL-----KNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYK 408
D K + L K +L+D + +K + +LP+ L +Q RF +
Sbjct: 311 -KDKKKLYECLDSFHKKEQLKD-FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHL 368
Query: 409 EKERINAKVLKDIKFPIEFDAYELCTPELQAK 440
N K+ I+FP + C+ + + K
Sbjct: 369 LNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDK 399
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 110 DLPAGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RD 164
D +GL N+G+TC+M++++QCL P +R ++ + +P + + +L +
Sbjct: 134 DGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHE 193
Query: 165 LYECMDNMKISPS 177
LY ++ + S S
Sbjct: 194 LYGALNTKQASSS 206
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLK 569
Y L +++HKG T + GHY+A+ K G W K +D V IS+EEVLK
Sbjct: 416 YELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 462
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 59/272 (21%), Positives = 113/272 (41%), Gaps = 31/272 (11%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RDLYE 245
+GL N+G+TC+M++++QCL P +R ++ + +P + + +L +LY
Sbjct: 142 SGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYG 201
Query: 246 CMDNMKISPSISP------FIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKT 299
++ + S S + FI L + + + Y QQDA+E W ++ +
Sbjct: 202 ALNTKQASSSSTSTNRQTGFIYL-----LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 256
Query: 300 A----LPGENEEGQDSAK--SSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYI 353
+ LP E + + K + F +++ + C + T + F LS I
Sbjct: 257 SYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTT-IDPFLDLSLDI 315
Query: 354 TTDVKYMLPGL-----KNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYK 408
D K + L K +L+D + +K + +LP+ L +Q RF +
Sbjct: 316 -KDKKKLYECLDSFHKKEQLKD-FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHL 373
Query: 409 EKERINAKVLKDIKFPIEFDAYELCTPELQAK 440
N K+ I+FP + C+ + + K
Sbjct: 374 LNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDK 404
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 110 DLPAGLNNLGNTCYMNAVIQCLKTVPE-LRKALKNLKGGLQPGSNPAQSITASL----RD 164
D +GL N+G+TC+M++++QCL P +R ++ + +P + + +L +
Sbjct: 139 DGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHE 198
Query: 165 LYECMDNMKISPS 177
LY ++ + S S
Sbjct: 199 LYGALNTKQASSS 211
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVK-KPNGTWIKCDDDKVYPISEEEVLKLSGGG 574
Y L AVL H G + GHYV ++ K +G W K DDD V ++EE ++ + GG
Sbjct: 241 YILHAVLVHSG-DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 58/245 (23%), Positives = 102/245 (41%), Gaps = 41/245 (16%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++
Sbjct: 7 VGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMP---TEGDDSSKSVPLALQRVF-----Y 58
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQD 310
++ S P ++ + F +T D S+MQ D E ++ ++ + G EG
Sbjct: 59 ELQHSDKPVGTKKLTKS----FGWETLD-SFMQHDVQELCRVLLDNVENKMKGTCVEGT- 112
Query: 311 SAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQD 370
I + F M + ++C E + + E + D++ + G KN +
Sbjct: 113 ------IPKLFRGKMVSYIQCKEVDYRSDRR--EDY--------YDIQLSIKGKKNIFES 156
Query: 371 QITKRS-PSLDRDAVY----------VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLK 419
+ + LD D Y K K LP L +Q +RF Y + N K+
Sbjct: 157 FVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKIND 216
Query: 420 DIKFP 424
+FP
Sbjct: 217 RFEFP 221
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLY 166
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++
Sbjct: 7 VGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMP---TEGDDSSKSVPLALQRVF 57
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVK-KPNGTWIKCDDDKVYPISEEEVLKLSGGG 574
Y L AVL H G + GHYV ++ K +G W K DDD V ++EE ++ + GG
Sbjct: 241 YILHAVLVHSG-DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 55/245 (22%), Positives = 96/245 (39%), Gaps = 41/245 (16%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL N G TCY N+++Q L +LRKA+ G + ++S+ +L+ ++
Sbjct: 7 VGLKNQGATCYXNSLLQTLFFTNQLRKAVYXXP---TEGDDSSKSVPLALQRVF-----Y 58
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQD 310
++ S P ++ + F +T D S+ Q D E ++ ++ G EG
Sbjct: 59 ELQHSDKPVGTKKLTKS----FGWETLD-SFXQHDVQELCRVLLDNVENKXKGTCVEGT- 112
Query: 311 SAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQD 370
I + F + ++C E + + E + D++ + G KN +
Sbjct: 113 ------IPKLFRGKXVSYIQCKEVDYRSDRR--EDY--------YDIQLSIKGKKNIFES 156
Query: 371 QITKRS-PSLDRDAVY----------VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLK 419
+ + LD D Y K K LP L +Q RF Y + N K+
Sbjct: 157 FVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKIND 216
Query: 420 DIKFP 424
+FP
Sbjct: 217 RFEFP 221
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRKAL 141
GL N G TCY N+++Q L +LRKA+
Sbjct: 7 VGLKNQGATCYXNSLLQTLFFTNQLRKAV 35
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVK-KPNGTWIKCDDDKVYPISEEEVLKLSGGG 574
Y L AVL H G + GHYV ++ K +G W K DDD V ++EE ++ + GG
Sbjct: 410 YILHAVLVHSG-DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 462
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 58/245 (23%), Positives = 102/245 (41%), Gaps = 41/245 (16%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++
Sbjct: 176 VGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMP---TEGDDSSKSVPLALQRVF-----Y 227
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQD 310
++ S P ++ + F +T D S+MQ D E ++ ++ + G EG
Sbjct: 228 ELQHSDKPVGTKKLTKS----FGWETLD-SFMQHDVQELCRVLLDNVENKMKGTCVEGT- 281
Query: 311 SAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQD 370
I + F M + ++C E + + E + D++ + G KN +
Sbjct: 282 ------IPKLFRGKMVSYIQCKEVDYRSDRR--EDY--------YDIQLSIKGKKNIFES 325
Query: 371 QITKRS-PSLDRDAVY----------VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLK 419
+ + LD D Y K K LP L +Q +RF Y + N K+
Sbjct: 326 FVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKIND 385
Query: 420 DIKFP 424
+FP
Sbjct: 386 RFEFP 390
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLY 166
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++
Sbjct: 176 VGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMP---TEGDDSSKSVPLALQRVF 226
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 147 GLQPGSNPAQSITASLRDLYECMDNMKISP-------SISPFIMLQGRYLPAGLNNLGNT 199
GL P +P + T + + C +IS +++P G L GL NLGNT
Sbjct: 13 GLVPRGSPTVTPTVNRENKPTCYPKAEISRLSASQIRNLNPVFGGSGPAL-TGLRNLGNT 71
Query: 200 CYMNAVIQCLKTVPEL 215
CYMN+++QCL P L
Sbjct: 72 CYMNSILQCLCNAPHL 87
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 19/25 (76%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPEL 137
GL NLGNTCYMN+++QCL P L
Sbjct: 63 TGLRNLGNTCYMNSILQCLCNAPHL 87
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 147 GLQPGSNPAQSITASLRDLYECMDNMKISP-------SISPFIMLQGRYLPAGLNNLGNT 199
GL P +P + T + + C +IS +++P G L GL NLGNT
Sbjct: 13 GLVPRGSPTVTPTVNRENKPTCYPKAEISRLSASQIRNLNPVFGGSGPAL-TGLRNLGNT 71
Query: 200 CYMNAVIQCLKTVPEL 215
CY N+++QCL P L
Sbjct: 72 CYXNSILQCLCNAPHL 87
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 18/25 (72%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPEL 137
GL NLGNTCY N+++QCL P L
Sbjct: 63 TGLRNLGNTCYXNSILQCLCNAPHL 87
>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 = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 34/135 (25%), Positives = 56/135 (41%), Gaps = 26/135 (19%)
Query: 192 GLNNLGNTCYMNAVIQCL-KTVPELRKALKNLKGGLQPGSNP-------AQSITASLRDL 243
GL NLGNT +MN+ +QCL T P LK+ NP A++ ++ +
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQM 69
Query: 244 YECMDNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPG 303
+ D ++P + + P+F+ Y QQD+ E +L L G
Sbjct: 70 WSGRD-----AHVAPRMFKTQVGRFAPQFS------GYQQQDSQE-------LLAFLLDG 111
Query: 304 ENEEGQDSAKSSFIE 318
+E+ K ++E
Sbjct: 112 LHEDLNRVKKKPYLE 126
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 498 TEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHYVAWVK-KPNGTWIKCDD 556
EF RG S ++ S Y L AV H G GHY A+ K K NG W DD
Sbjct: 277 VEFPIRGLNMSEFVCNL-SARPYVYDLIAVSNHYG-AMGVGHYTAYAKNKLNGKWYYFDD 334
Query: 557 DKVYPISEEEVL 568
V SE++++
Sbjct: 335 SNVSLASEDQIV 346
Score = 32.7 bits (73), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPEL 137
GL NLGNT +MN+ +QCL L
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPL 33
>pdb|1V86|A Chain A, Solution Structure Of The Ubiquitin Domain From Mouse
D7wsu128e Protein
Length = 95
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 28/46 (60%)
Query: 36 FKAQLYELTGVQIDRQKVMCKGATLKNDEWDNFKLSNGSMVLLMGS 81
K +++ +TG+ QKVM KG ++ K+++G+ ++++GS
Sbjct: 42 LKQKIHSITGLPPAMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGS 87
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,648,321
Number of Sequences: 62578
Number of extensions: 679191
Number of successful extensions: 1620
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1547
Number of HSP's gapped (non-prelim): 57
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)