RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7711
(577 letters)
>2ayn_A Ubiquitin carboxyl-terminal hydrolase 14; deubiquitinating enzymes,
DUB, USP14, proteasome, enzyme mechanism; 3.20A {Homo
sapiens} SCOP: d.3.1.9 PDB: 2ayo_A
Length = 404
Score = 327 bits (840), Expect = e-107
Identities = 198/400 (49%), Positives = 256/400 (64%), Gaps = 46/400 (11%)
Query: 189 LPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPA--QSITASLRDLYEC 246
LP GL NLGNTCYMNA +QC+++VPEL+ ALK G L+ A Q ITA+LRDL++
Sbjct: 13 LPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDS 72
Query: 247 MDNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENE 306
MD K S SI P I+LQ LH FP+FA+K + G Y+QQDANECW +M+R+L+ L +
Sbjct: 73 MD--KTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIED 130
Query: 307 EGQDSAKS------------SFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYIT 354
+ S 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 AKVLKDIKFPIEFDAYELCTPELQAKLAPMREKFKIAEEKEAFEEFRTQYVFISIPMDEI 474
AKVLKD+KFP+ D YELCTPELQ K+ R KFK E+K+ ++ T
Sbjct: 251 AKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSD---------- 300
Query: 475 YVRFGQKIYAPVGDRIQDFGVKSTEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRT 534
KS+ + DIGSNN GYY LQAVLTH+GR+
Sbjct: 301 --------------------KKSSPQKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRS 340
Query: 535 SSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLKLSGGG 574
SSSGHYV+WVK+ WIK DDDKV ++ E++L+LSGGG
Sbjct: 341 SSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGG 380
>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9
Length = 415
Score = 264 bits (675), Expect = 6e-83
Identities = 108/397 (27%), Positives = 188/397 (47%), Gaps = 26/397 (6%)
Query: 188 YLPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKG------GLQPGSNPAQSITASLR 241
LP G N+GNTCY+NA +Q L V +LR + N + I ++
Sbjct: 22 QLPVGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSNSGAQDEEIHKQIVIEMK 81
Query: 242 DLYECMDNMKISPSISPFIMLQVLHNVFPRFADKTDDG-SYMQQDANECWTEMVRMLKTA 300
+E + N K S+ P ++L L +P+FA++ G Y QQDA E +T++ +
Sbjct: 82 RCFENLQN-KSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLFHSMSIV 140
Query: 301 LPGENEEGQDSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYM 360
+ + F T +K + ++ + K ES +L C+I+ +M
Sbjct: 141 FGDK------------FSEDFRIQFKTTIKDTANDNDITVKENESDSKLQCHISGTTNFM 188
Query: 361 LPGLKNKLQDQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKD 420
GL L ++I KRS +++Y K+SRLP +LT+Q+VRFF+K +K+L+
Sbjct: 189 RNGLLEGLNEKIEKRSDLTGANSIYSVEKKISRLPKFLTVQYVRFFWKRSTNKKSKILRK 248
Query: 421 IKFPIEFDAYELCTPELQAKLAPMREKFKIAEEKEAFEEFRTQYVFISIPMDEIYVRFGQ 480
+ FP + D ++ TPE A+ +R++ + E+++ +E + E + +
Sbjct: 249 VVFPFQLDVADMLTPEYAAEKVKVRDELRKVEKEKNEKEREIKRRKFDPSSSENVMTPRE 308
Query: 481 KIYAPVGDRIQDFGVKSTEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHY 540
+ V + ++ + P ++ G N S Y L V+TH+G S SGHY
Sbjct: 309 QYETQVALNESE----KDQWLEEYKKHFPPNLEKGENPSCVYNLIGVITHQGANSESGHY 364
Query: 541 VAWVKKP--NGTWIKCDDDKVYPISEEEVLKLSGGGK 575
A+++ W K +DDKV + +E++ L+GGG+
Sbjct: 365 QAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGE 401
Score = 90.3 bits (223), Expect = 1e-19
Identities = 26/99 (26%), Positives = 40/99 (40%), Gaps = 7/99 (7%)
Query: 93 KPKFVEDMNESERAVSLDLPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKG------ 146
K E + LP G N+GNTCY+NA +Q L V +LR + N
Sbjct: 5 KIHHHHHHPEQQVQQFAQLPVGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSN 64
Query: 147 GLQPGSNPAQSITASLRDLYECMDNMKISPSISPFIMLQ 185
+ I ++ +E + N K S+ P ++L
Sbjct: 65 SGAQDEEIHKQIVIEMKRCFENLQN-KSFKSVLPVVLLN 102
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol
protease, UBL conjugation pathway, metal-binding,
zinc-finger,structural genomics; 2.80A {Homo sapiens}
Length = 854
Score = 104 bits (260), Expect = 1e-23
Identities = 59/369 (15%), Positives = 124/369 (33%), Gaps = 56/369 (15%)
Query: 122 CYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDNMKISPSISPF 181
Y + P L + L + + +++ + ++ +
Sbjct: 279 SYDE---DDMVLDPSLAEHLSHFGIDMLKMQKTDKTM--TELEIDMNQRIGEWELIQESG 333
Query: 182 IMLQGRYLPA--GLNNLGNTCYMNAVIQCLKTVPELRKALKNL--KGGLQPGSNPAQSIT 237
+ L+ + P G+ NLGN+CY+N+V+Q L ++P+ ++ + K ++P Q +
Sbjct: 334 VPLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFS 393
Query: 238 ASLRDLYECM-------------------DNMKISPSISPFIMLQVLHNVFPRFADKTDD 278
+ L + + ++ I+P + ++ P F+
Sbjct: 394 TQVAKLGHGLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFS----- 448
Query: 279 GSYMQQDANECWTEMVRMLKTALPGENE------------------EGQDSAKSSFIEQY 320
+ QQDA E + ++ M++ E +
Sbjct: 449 -TNRQQDAQEFFLHLINMVERNCRSSENPNEVFRFLVEEKIKCLATEKVKYTQRVDYIMQ 507
Query: 321 FYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKL--QDQITK-RSP 377
MD L E K ++++ + +Q+ S
Sbjct: 508 LPVPMDAALNKEELLEYEEKKRQAEEEKMALPELVRAQVPFSSCLEAYGAPEQVDDFWST 567
Query: 378 SLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIEFDAYELCTPEL 437
+L +V VKT++ + P YL IQ + F + + K+ I+ P E D +L L
Sbjct: 568 ALQAKSVAVKTTRFASFPDYLVIQI-KKFTFGLDWVPKKLDVSIEMPEELDISQLRGTGL 626
Query: 438 QAKLAPMRE 446
Q + +
Sbjct: 627 QPGEEELPD 635
Score = 61.1 bits (147), Expect = 6e-10
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 1/78 (1%)
Query: 488 DRIQDFGVKSTEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP 547
D + + S + G Y L A ++H G ++ GHYV +KK
Sbjct: 763 DAEAAMDISEGRSAADSISESVPVGPKVRDGPGKYQLFAFISHMGTSTMCGHYVCHIKK- 821
Query: 548 NGTWIKCDDDKVYPISEE 565
G W+ +D KV +
Sbjct: 822 EGRWVIYNDQKVCASEKP 839
>3nhe_A Ubiquitin carboxyl-terminal hydrolase 2; cysteine protease,
substrate ENZY complex, hydrolase-protein binding
complex; HET: CME; 1.26A {Homo sapiens} PDB: 2hd5_A
2ibi_A
Length = 348
Score = 96.8 bits (241), Expect = 5e-22
Identities = 58/281 (20%), Positives = 91/281 (32%), Gaps = 68/281 (24%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRKAL--KNLKGGLQPGSNPAQSITASLRDLYECMD 248
AGL NLGNTC+MN+++QCL ELR + L GSN ++ L + +
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 249 NMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTAL------- 301
+ +SP + PRF Y QQDA E ++ L +
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFVG------YNQQDAQEFLRFLLDGLHNEVNRVTLRP 123
Query: 302 ---PGENEEGQDSAKS------------SFIEQYFYTIMDTELKCS----ESET-EP--- 338
P + D K S I F + + L C+ S +P
Sbjct: 124 KSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWD 183
Query: 339 -----PTKGTESFQQLSC--------YITTDVKYMLPGLKNKLQDQITKRSPSLDRDAVY 385
+G + C + D K + + +
Sbjct: 184 LSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGR-------------KRC-- 228
Query: 386 VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIE 426
+K + R P L + RF E +K+ + FP+
Sbjct: 229 IKKFSIQRFPKILVLHLKRF--SESRIRTSKLTTFVNFPLR 267
Score = 62.9 bits (153), Expect = 7e-11
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEVLK 569
+ N Y L AV H G T+ GHY A+ + P G W +D V P+S +V
Sbjct: 278 NTNHAVYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRT 331
>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific
protease 14, USP14, ubiquitin-like fold, structural
genomics; NMR {Mus musculus} SCOP: d.15.1.1
Length = 96
Score = 89.5 bits (222), Expect = 7e-22
Identities = 50/84 (59%), Positives = 61/84 (72%), Gaps = 2/84 (2%)
Query: 11 TYIVKVKWGKETFE-VDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDEWDNFK 69
Y V VKWGKE FE V+++TDE PM+FKAQL+ LTGVQ RQKVM KG TLK+D+W N K
Sbjct: 7 GYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDDDWGNIK 66
Query: 70 LSNGSMVLLMGSKEEDSMKEPVVK 93
+ NG VL+MGS + +EP K
Sbjct: 67 MKNGMTVLMMGSADALP-EEPSAK 89
>1v86_A DNA segment, CHR 7, wayne state university 128, expressed;
ubiquitin fold, structural genomics, D7WSU128E protein;
HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1
Length = 95
Score = 88.7 bits (220), Expect = 1e-21
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDEWDNFKLSNG 73
+K+ W K +V V D K +++ +TG+ QKVM KG ++ K+++G
Sbjct: 20 LKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTLREIKVTSG 79
Query: 74 SMVLLMGSKEE 84
+ ++++GS
Sbjct: 80 AKIMVVGSTIS 90
>3i3t_A Ubiquitin carboxyl-terminal hydrolase 21; hydrolase, structural
genomics consortium, SGC, activator, alternative
splicing, chromatin regulator, nucleus, polymorphism,
protease; 2.59A {Homo sapiens} PDB: 2y5b_A 3mtn_A
Length = 355
Score = 95.5 bits (237), Expect = 1e-21
Identities = 61/285 (21%), Positives = 90/285 (31%), Gaps = 60/285 (21%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRKA-LKNLKGGLQPGSNPAQSITASLRDLYECMDNM 250
GL NLGNTC++NAV+QCL + LR L+ PG AQ +T + D+ + +
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 251 KISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTAL--------- 301
+++P V P F+ Y QQDA E ++ L +
Sbjct: 65 DSCEAVNPTRFRAVFQKYVPSFSG------YSQQDAQEFLKLLMERLHLEINRRGRRAPP 118
Query: 302 ----------------PGENEEGQDSAKS------------SFIEQYFYTIMDTELKCSE 333
E E D ++ S I F + + LKC
Sbjct: 119 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 178
Query: 334 SETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQDQITKRSPSLDRDAVY-------- 385
+ E F LS I + TK L+ +
Sbjct: 179 CGYR--STTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEE-ELESENAPVCDRCRQK 235
Query: 386 ---VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIEF 427
K V R P L + RF K + FP++
Sbjct: 236 TRSTKKLTVQRFPRILVLHLNRFSASRGSIK--KSSVGVDFPLQR 278
Score = 55.4 bits (133), Expect = 2e-08
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 515 GSNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKVYPISEEEVLK 569
S Y L A+ H G + GHY A + G W +D +V P+SE +V
Sbjct: 287 DKAGSPVYQLYALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVAS 339
>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex,
hydrolase-transcription regulator-Pro binding complex,
acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae}
PDB: 3mhh_A 3m99_A
Length = 476
Score = 95.8 bits (238), Expect = 3e-21
Identities = 53/299 (17%), Positives = 105/299 (35%), Gaps = 60/299 (20%)
Query: 165 LYECMDNMKISPSISPFIMLQGRYLPAGLNNLGNTCYMNAVIQCLKTVPELRKAL----- 219
L + D++ + G +GL N+G+TC+M++++QCL P +
Sbjct: 119 LAKYWDDVCTKTMVPSMERRDG---LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIH 175
Query: 220 KNLKGGLQPGSNPAQSITASLRDLYECMDNMKISPS-------ISPFIMLQVLHNVFPRF 272
N P + ++ + +LY ++ + S S +L +
Sbjct: 176 SNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNL 235
Query: 273 ADKTDDGSYMQQDANECWT----EMVRMLKTALPGENEEGQDSAKS--SFIEQYFYTIMD 326
A Y QQDA+E W ++ + LP E + + K + F ++
Sbjct: 236 A------GYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLE 289
Query: 327 TELKC------SESETEP------PTKGTESFQQ-LSCYITTDV----KYMLPGLKNKLQ 369
+ + C S++ +P K + + L + + Y +
Sbjct: 290 SSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNST-- 347
Query: 370 DQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIEFD 428
+DA+ K + +LP+ L +Q RF + K+ I+FP +
Sbjct: 348 -----------QDAI--KQLGIHKLPSVLVLQLKRFEHLLNGSNR-KLDDFIEFPTYLN 392
Score = 74.2 bits (182), Expect = 3e-14
Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 505 QGSSPGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKPNGTWIKCDDDKVYPISE 564
+ G Y L +++HKG T + GHY+A+ K G W K +D V IS+
Sbjct: 399 TKEKDKHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQ 457
Query: 565 EEVLK 569
EEVLK
Sbjct: 458 EEVLK 462
Score = 51.5 bits (123), Expect = 5e-07
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 112 PAGLNNLGNTCYMNAVIQCLKTVPELRKAL-----KNLKGGLQPGSNPAQSITASLRDLY 166
+GL N+G+TC+M++++QCL P + N P + ++ + +LY
Sbjct: 141 LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELY 200
Query: 167 ECMDNMKISPS 177
++ + S S
Sbjct: 201 GALNTKQASSS 211
>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination,
hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9
PDB: 1nbf_A
Length = 353
Score = 91.9 bits (228), Expect = 2e-20
Identities = 54/259 (20%), Positives = 94/259 (36%), Gaps = 43/259 (16%)
Query: 190 PAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDN 249
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++ + +
Sbjct: 6 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT---EGDDSSKSVPLALQRVFYELQH 62
Query: 250 MKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQ 309
+ S+MQ D E ++ ++ + G EG
Sbjct: 63 SDKPVGTKKLT----------KSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEG- 111
Query: 310 DSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQ 369
I + F M + ++C E + + E + + +K G KN +
Sbjct: 112 ------TIPKLFRGKMVSYIQCKEVDYRSDRR--EDYYDIQL----SIK----GKKN-IF 154
Query: 370 DQITK--RSPSLDRDAVY----------VKTSKVSRLPAYLTIQFVRFFYKEKERINAKV 417
+ LD D Y K K LP L +Q +RF Y + N K+
Sbjct: 155 ESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKI 214
Query: 418 LKDIKFPIEFDAYELCTPE 436
+FP + E
Sbjct: 215 NDRFEFPEQLPLDEFLQKT 233
Score = 58.0 bits (140), Expect = 3e-09
Identities = 26/157 (16%), Positives = 55/157 (35%), Gaps = 21/157 (13%)
Query: 112 PAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDN 171
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++ + +
Sbjct: 6 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT---EGDDSSKSVPLALQRVFYELQH 62
Query: 172 MKISPSISPFI-MLQGRYLPAGL---NNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQ 227
L + + ++ V +K + + L G
Sbjct: 63 SDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKG-TCVEGTIPKLFRG-- 119
Query: 228 PGSNPAQSITASLRDLYECMDNMKISPSISPFIMLQV 264
+ +C + S + +Q+
Sbjct: 120 -----------KMVSYIQCKEVDYRSDRREDYYDIQL 145
Score = 56.0 bits (135), Expect = 1e-08
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 516 SNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEVLKLSGGG 574
+ Y L AVL H G + GHYV ++ +G W K DDD V ++EE ++ + GG
Sbjct: 235 PKDPANYILHAVLVHSG-DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
>2kd0_A LRR repeats and ubiquitin-like domain-containing protein
AT2G30105; ubiquitin-like protein, NESG, leucine-rich
repeat, structural genomics; NMR {Arabidopsis thaliana}
Length = 85
Score = 84.6 bits (210), Expect = 2e-20
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 7 KPPHTYIVKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-W 65
T + VK+G ++ + V D K+QL +T V QK++ KG L
Sbjct: 8 HSHSTIKLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTL 67
Query: 66 DNFKLSNGSMVLLMGSK 82
+ +G+ ++LM S+
Sbjct: 68 KQSDVGSGAKLMLMASQ 84
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 93.1 bits (231), Expect = 4e-20
Identities = 54/258 (20%), Positives = 94/258 (36%), Gaps = 43/258 (16%)
Query: 190 PAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDN 249
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++ + +
Sbjct: 175 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT---EGDDSSKSVPLALQRVFYELQH 231
Query: 250 MKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQ 309
+ S+MQ D E ++ ++ + G EG
Sbjct: 232 SDKPVGTKKLT----------KSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEG- 280
Query: 310 DSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQ 369
I + F M + ++C E + + E + + +K G KN +
Sbjct: 281 ------TIPKLFRGKMVSYIQCKEVDYRSDRR--EDYYDIQL----SIK----GKKN-IF 323
Query: 370 DQITK--RSPSLDRDAVY----------VKTSKVSRLPAYLTIQFVRFFYKEKERINAKV 417
+ LD D Y K K LP L +Q +RF Y + N K+
Sbjct: 324 ESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKI 383
Query: 418 LKDIKFPIEFDAYELCTP 435
+FP + E
Sbjct: 384 NDRFEFPEQLPLDEFLQK 401
Score = 56.1 bits (135), Expect = 2e-08
Identities = 26/157 (16%), Positives = 56/157 (35%), Gaps = 21/157 (13%)
Query: 112 PAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDN 171
GL N G TCYMN+++Q L +LRKA+ + G + ++S+ +L+ ++ + +
Sbjct: 175 YVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT---EGDDSSKSVPLALQRVFYELQH 231
Query: 172 MKISPSISPFI-MLQGRYLPAGLNNLG---NTCYMNAVIQCLKTVPELRKALKNLKGGLQ 227
L + + + ++ V +K + + L G
Sbjct: 232 SDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKG-TCVEGTIPKLFRG-- 288
Query: 228 PGSNPAQSITASLRDLYECMDNMKISPSISPFIMLQV 264
+ +C + S + +Q+
Sbjct: 289 -----------KMVSYIQCKEVDYRSDRREDYYDIQL 314
Score = 56.1 bits (135), Expect = 2e-08
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEVLKLSGGG 574
Y L AVL H G + GHYV ++ +G W K DDD V ++EE ++ + GG
Sbjct: 410 YILHAVLVHSG-DNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 462
>2gfo_A Ubiquitin carboxyl-terminal hydrolase 8; protease, thiol protease,
UBL conjugation pathway deubiquitinating enzyme, DUB,
zinc ribbon; 2.00A {Homo sapiens} SCOP: d.3.1.9 PDB:
3n3k_A
Length = 396
Score = 89.6 bits (222), Expect = 2e-19
Identities = 55/273 (20%), Positives = 94/273 (34%), Gaps = 53/273 (19%)
Query: 191 AGLNNLGNTCYMNAVIQCLKTVPELRKA-LKNLKGGLQPGSNPAQS---ITASLRDLYEC 246
GL NLGNTCYMN+++QCL P L +N SN + + +
Sbjct: 63 TGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKA 122
Query: 247 MDNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRML--------- 297
+ + ISP + + +FA Y QQD+ E ++ L
Sbjct: 123 LWTGQYRY-ISPKDFKITIGKINDQFAG------YSQQDSQELLLFLMDGLHEDLNKADN 175
Query: 298 KTALPGENEEGQDSAKS-------------SFIEQYFYTIMDTELKCSESETEPPTKGTE 344
+ EN + D K+ S I F + ++C + T E
Sbjct: 176 RKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRT--FE 233
Query: 345 SFQQLSCYITTDVKYMLPGLKNKLQDQITKRSPSLDRDAVY-----------VKTSKVSR 393
+F Y++ + +K L + + +K ++ +
Sbjct: 234 AF----MYLSLPLASTSKCTLQDCLRLFSK-EEKLTDNNRFYCSHCRARRDSLKKIEIWK 288
Query: 394 LPAYLTIQFVRFFYKEKERINAKVLKDIKFPIE 426
LP L + RF Y + + K+ + FP+E
Sbjct: 289 LPPVLLVHLKRFSYDGRWK--QKLQTSVDFPLE 319
Score = 54.9 bits (132), Expect = 3e-08
Identities = 16/27 (59%), Positives = 19/27 (70%)
Query: 113 AGLNNLGNTCYMNAVIQCLKTVPELRK 139
GL NLGNTCYMN+++QCL P L
Sbjct: 63 TGLRNLGNTCYMNSILQCLCNAPHLAD 89
Score = 53.4 bits (128), Expect = 9e-08
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 522 YTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEVLK 569
Y L +V H G GHY A+ K W K DD +V IS V
Sbjct: 337 YNLFSVSNHYG-GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKS 384
>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1 PDB: 2kx3_A
Length = 90
Score = 75.7 bits (186), Expect = 3e-17
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 14 VKVKWGKETFEVD-VDTDEEPMLFKAQLYELTGVQIDRQKVM---CKGATLKNDE-WDNF 68
+ VKWG + + V + D+ + K L LTGV +RQK++ KG +ND
Sbjct: 10 IIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL 69
Query: 69 KLSNGSMVLLMGSKEED 85
KL + +++MG++E
Sbjct: 70 KLKPNTKIMMMGTRESG 86
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 78.1 bits (192), Expect = 1e-15
Identities = 56/286 (19%), Positives = 90/286 (31%), Gaps = 64/286 (22%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQ---PGSNPAQS---ITASLRDLYE 245
GL NLGNTC+MN+ +QCL L LK + NP I + +L +
Sbjct: 10 GLGNLGNTCFMNSALQCLSNTAPLTDYF--LKDEYEAEINRDNPLGMKGEIAEAYAELIK 67
Query: 246 CMDNMKISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWT--------EMVRML 297
M + + + ++P + + P+F+ Y QQD+ E ++ R+
Sbjct: 68 QMWSGRDAH-VAPRMFKTQVGRFAPQFSG------YQQQDSQELLAFLLDGLHEDLNRVK 120
Query: 298 KTALPGENEEGQDSAK--------------SSFIEQYFYTIMDTELKCSESETEPPTKGT 343
K + S I F+ + + L C E T
Sbjct: 121 KKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVT--F 178
Query: 344 ESFQQLS----------CYITTDVKYMLPGLKNKLQDQITK--RSPSLDRDAVY------ 385
+ F L+ L+D I +L +
Sbjct: 179 DPFCYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCK 238
Query: 386 -----VKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIE 426
K + LP L + RF Y R K+ ++FPI
Sbjct: 239 KHQQATKKFDLWSLPKILVVHLKRFSYNRYWR--DKLDTVVEFPIR 282
Score = 58.8 bits (142), Expect = 2e-09
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 515 GSNNSGYYTLQAVLTHKGRTSSSGHYVAWVKKP-NGTWIKCDDDKVYPISEEEVLK 569
S Y L AV H G GHY A+ K NG W DD V SE++++
Sbjct: 293 LSARPYVYDLIAVSNHYGAMGV-GHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVT 347
Score = 45.3 bits (107), Expect = 4e-05
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 114 GLNNLGNTCYMNAVIQCLKTVPELRKALKN 143
GL NLGNTC+MN+ +QCL L
Sbjct: 10 GLGNLGNTCFMNSALQCLSNTAPLTDYFLK 39
>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}
Length = 320
Score = 75.6 bits (185), Expect = 4e-15
Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 4/93 (4%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKV---MCKGATLKNDEW-DNFK 69
V VKW + + VD+ + + + +++ T V+ +RQK+ KG T ++ +
Sbjct: 8 VIVKWSGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALE 67
Query: 70 LSNGSMVLLMGSKEEDSMKEPVVKPKFVEDMNE 102
L ++++GS E D + E +++
Sbjct: 68 LKPNFKLMMVGSTEADIEDACSLPDNIGEVVDD 100
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 65.5 bits (159), Expect = 3e-11
Identities = 86/521 (16%), Positives = 144/521 (27%), Gaps = 185/521 (35%)
Query: 65 WDNFKLSNGSMVLLMGSKEEDSMKEPVVKP-------KFVEDMNESERAVSLD--LPAGL 115
+ F L ++ + EP +V + E + D L L
Sbjct: 34 QEQFNKI-----LPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 116 NNLGNTCYM-----NAVIQCL-----KTVPELRKALKN----LKGGLQPGSNPAQS--IT 159
CY+ +A+ L T+ + ++ +KN +P + S
Sbjct: 89 TEF-ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR 147
Query: 160 AS-----------------------LRDLYECMDNMKISPS-ISPFI-----MLQG---- 186
A LRDLY+ + I L
Sbjct: 148 AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ------TYHVLVGDLIKFSAETLSELIRT 201
Query: 187 -----RYLPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLR 241
+ GLN + + L+N P + P + S
Sbjct: 202 TLDAEKVFTQGLN--------------------ILEWLEN------PSNTPDKDYLLS-- 233
Query: 242 DLYECMDNMKISPSIS-PFI-MLQVLH-NVFPRFADKT-DDGSYMQQDANECWTEMVRML 297
P IS P I ++Q+ H V + T + + A +V +
Sbjct: 234 -----------IP-ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAV 281
Query: 298 KTALPGENEEGQDSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDV 357
A E S + I F+ ++C E P T S + S V
Sbjct: 282 AIAETDSWESFFVSVR-KAITVLFF----IGVRC--YEAYPNTSLPPSILEDSLENNEGV 334
Query: 358 K-YML--PGL-KNKLQDQITKRSPSLDRDAV-----------YVKTSKVSRLPAYLTIQF 402
ML L + ++QD + K + L V VS P L
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV----VSGPPQSL---- 386
Query: 403 VRFFYKEKERINAKVLKDIKFPIEFDAYELCTPELQAKLAPMREKFKIAEEKEAFEEFRT 462
+N L+ K P D Q++ P E+ K+ F
Sbjct: 387 --------YGLNLT-LRKAKAPSGLD---------QSR-IPFSER-KLK--------FSN 418
Query: 463 QYVFISIPMDEIYVRFGQKIYAPVGDRI-QDFGVKSTEFQS 502
+++ ++ P F + P D I +D + F +
Sbjct: 419 RFLPVASP-------FHSHLLVPASDLINKDLVKNNVSFNA 452
Score = 53.5 bits (128), Expect = 2e-07
Identities = 56/325 (17%), Positives = 101/325 (31%), Gaps = 131/325 (40%)
Query: 33 PMLFKAQL--YELT----GVQIDRQKVMCKGATLKN------------DEWDNF-KLSNG 73
P++ QL Y +T G + KGAT + D W++F
Sbjct: 239 PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRK 298
Query: 74 SMVLL--MGSKEEDSMKEPVVKPKFVEDMNESERAVSLDLPAGLNNLGNTCYMNAV---- 127
++ +L +G + ++ + P +ED SL+ NN G M ++
Sbjct: 299 AITVLFFIGVRCYEAYPNTSLPPSILED--------SLE-----NNEGVPSPMLSISNLT 345
Query: 128 ---IQCL-----KTVPELRK---ALKN------LKGGLQPGSNPAQSITA---SLRDLYE 167
+Q +P ++ +L N + G P QS+ +LR
Sbjct: 346 QEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSG-------PPQSLYGLNLTLRKAKA 398
Query: 168 C--MDNMKISPSISPF----IMLQGRYLPAGLNNLGNTCYMNAVIQCLKTVPE----LRK 217
+D +I PF + R+LP + P L
Sbjct: 399 PSGLDQSRI-----PFSERKLKFSNRFLP---------------V----ASPFHSHLLVP 434
Query: 218 ALKNLKGGLQPGSNPAQSITASLRDLYECMDNMKISPSISPFIMLQVLHNVFPRFADKTD 277
A + L +++ + +D+ +I P V T
Sbjct: 435 ASDLINKDLV-----KNNVSFNAKDI-------QI-----P-----VYD---------TF 463
Query: 278 DGSYMQQDANECWTEMVRMLKTALP 302
DGS ++ + +V + LP
Sbjct: 464 DGSDLRVLSGSISERIVDCI-IRLP 487
Score = 35.8 bits (82), Expect = 0.044
Identities = 45/268 (16%), Positives = 78/268 (29%), Gaps = 88/268 (32%)
Query: 310 DSAKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQ 369
+ A + F + Y ++I+D P T F G K K
Sbjct: 1647 NRADNHFKDTYGFSILDI-------VINNPVNLTIHF---------------GGEKGK-- 1682
Query: 370 DQITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRF-FYKEKERINA------------- 415
+I + ++ + + K ++ + + F EK ++A
Sbjct: 1683 -RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEK 1741
Query: 416 ---KVLKDIKFPIEFDAY-------E---LC------TPELQAKLAPMREKFKIAEEKEA 456
+ LK K I DA E L + E ++ R +
Sbjct: 1742 AAFEDLKS-KGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMT-MQVAVPR 1799
Query: 457 FEEFRTQYVFISIPMDEIYVRFGQKIYAPVGDRIQDFGVKSTEFQSRGQGSSPGRVDIGS 516
E R+ Y I+I + F Q+ V +R+ G ++ V+I
Sbjct: 1800 DELGRSNYGMIAINPGRVAASFSQEALQYVVERV---GKRTGWL-----------VEI-V 1844
Query: 517 N-NS-GYYTLQAVLTHKGRTSSSGHYVA 542
N N Q V +G A
Sbjct: 1845 NYNVEN---QQYVA--------AGDLRA 1861
>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics,
apoptosis, riken structural genomics/proteomics
initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP:
d.15.1.1
Length = 92
Score = 57.1 bits (137), Expect = 2e-10
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 14 VKVKWGKETFEVDVDTD---EEPML--FKAQLYELTGVQIDRQKVMCKGATLKNDE--WD 66
V V E ++ V + EP++ + E+ GV QK++ KG +LK E
Sbjct: 10 VTVTHSNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLS 69
Query: 67 NFKLSNGSMVLLMGSKEE 84
+ +G V+L+G K
Sbjct: 70 ALGIQDGCRVMLIGKKNS 87
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 62.2 bits (150), Expect = 3e-10
Identities = 99/594 (16%), Positives = 182/594 (30%), Gaps = 184/594 (30%)
Query: 6 GKPPHTY--IVKVKWGKETFEVDVD----TDEEPMLFKA--------------QLYELTG 45
G+ + Y I+ V ++ F + D D + L
Sbjct: 12 GEHQYQYKDILSVF--EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 46 VQIDRQKVMCK---GATLKND-EWDNFKLSNGSMVLLMGSKEEDSMKEPVVKPKFVEDMN 101
+ +Q+ M + L+ + ++ LM +K +P + M
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKF------------LM-----SPIKTEQRQPSMMTRMY 112
Query: 102 ESERAVSLDLPAGLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPA------ 155
+R L N N + + L+ +LR+AL L+P N
Sbjct: 113 IEQRDR-------LYN-DNQVFAKYNVSRLQPYLKLRQALLE----LRPAKNVLIDGVLG 160
Query: 156 ---QSITAS-LRDL-YECMDNMKISPSISPFIMLQGRYLPAGLNNLGNTCYMNAVIQCLK 210
+ +C + KI F +L NL N V++ L+
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKI------F------WL-----NLKNCNSPETVLEMLQ 203
Query: 211 TVPELRKALKNLKGGLQPGSNP---AQSITASLRDL-----YE-C---MDNMKISPSISP 258
+ L + N SN SI A LR L YE C + N++ + + +
Sbjct: 204 KL--LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261
Query: 259 F-IMLQVLHNVFPRFADKTDDGS------YMQQDANECWTE---------MVRMLKTALP 302
F + ++L + RF TD S + T + LP
Sbjct: 262 FNLSCKIL--LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 303 GENEEG-------------QDSAKSSFIEQYFYTIMDTELKCSESETEPP-TKGTESFQQ 348
E A + + T ++ S + EP + + F +
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR--KMFDR 377
Query: 349 LSCY-----ITTDVKYML-PGLKNKLQDQIT----KRSPSLDRDAVYVKTSKVSRLPA-Y 397
LS + I T + ++ + + K S +++ K S +S +P+ Y
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS-LVEKQP---KESTIS-IPSIY 432
Query: 398 LTIQFVRFFYKEKERINAKVLKDIKFPIEFDAYELCTPELQAKLAPMREKF--------K 449
L ++ + + ++ ++ P FD+ +L P + + F K
Sbjct: 433 LELKVKL---ENEYALHRSIVDHYNIPKTFDSDDLIPP-------YLDQYFYSHIGHHLK 482
Query: 450 IAEEKEAFEEFRTQYVFISIPMDEIYVRF-GQKI---------YAPVGDRIQDF 493
E E FR + +D RF QKI + + +Q
Sbjct: 483 NIEHPERMTLFRMVF------LD---FRFLEQKIRHDSTAWNASGSILNTLQQL 527
>2vhf_A Ubiquitin carboxyl-terminal hydrolase CYLD; cytokine signalling,
linkage specificity, deubiquitinating enzyme, Lys63-
linked, anti-oncogene; 2.8A {Homo sapiens}
Length = 374
Score = 47.5 bits (112), Expect = 7e-06
Identities = 60/372 (16%), Positives = 104/372 (27%), Gaps = 81/372 (21%)
Query: 192 GLNNLGNTCYMNAVIQCLKTVPELRKALKNLKGGLQPGSNPAQSITASLRDLYECMDNMK 251
G+ N+CY+++ + CL + + L + S T L L + N
Sbjct: 11 GIQGHYNSCYLDSTLFCLFAFSSVLDTV--LLRPKEKNDVEYYSETQEL--LRTEIVNPL 66
Query: 252 ISPSISPFIMLQVLHNVFPRFADKTDDGSYMQQDANECWTEMVRMLKTALPGENEEGQDS 311
+ L + + + ++D E + + P
Sbjct: 67 RIYGYVCATKIMKLRKILEKVEA-ASGFTSEEKDPEEFLNILFHHILRVEPLLKIRSAGQ 125
Query: 312 AKSSFIEQYFYTIMDTELKCSESETEPPTKGTESFQQLSCYITTDVKYMLPGLKNKLQDQ 371
+ YFY I + + PT QQL
Sbjct: 126 KVQ---DCYFYQIFMEK----NEKVGVPT-----IQQL---------------------- 151
Query: 372 ITKRSPSLDRDAVYVKTSKVSRLPAYLTIQFVRFFYKEKERINAKVLKDIKFPIEFDAYE 431
L+ + K + P+ L IQ RF + K+ K I +E + +
Sbjct: 152 -------LEWSFINSNL-KFAEAPSCLIIQMPRF------GKDFKLFKKIFPSLELNITD 197
Query: 432 LCTP-----ELQAKLAPMREKFKIAEEKEAFEEFRTQYVFISIPMDEIYVRFGQKIYAPV 486
L + LA E + ++ + Q+ ++ + Y PV
Sbjct: 198 LLEDTPRQCRICGGLAMY-ECRECYDDPDISAGKIKQFCKTCNTQVHLHPKRLNHKYNPV 256
Query: 487 GDRIQDFGVKSTEFQSRGQGSSPGRVDIGSNNSGYYTLQAVLTHKGRTSSSGHYVAWVK- 545
S + G L AVL + HYVA+VK
Sbjct: 257 ---------------SLPKDLPDWDWRHGCIPCQNMELFAVL-----CIETSHYVAFVKY 296
Query: 546 -KPNGTWIKCDD 556
K + W+ D
Sbjct: 297 GKDDSAWLFFDS 308
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 44.9 bits (105), Expect = 9e-06
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 138 RKALKNLKGGLQ---PGSNPAQSITASL 162
++ALK L+ L+ S PA +I A++
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATM 46
Score = 44.9 bits (105), Expect = 9e-06
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 216 RKALKNLKGGLQ---PGSNPAQSITASL 240
++ALK L+ L+ S PA +I A++
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATM 46
Score = 30.7 bits (68), Expect = 0.76
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 18/46 (39%)
Query: 453 EKEAFEEFRTQYVFISIPMDEIYVRFGQKIYAPVGDRIQDFGVKST 498
EK+A ++ + S+ K+YA D +K+T
Sbjct: 18 EKQALKKLQA-----SL-----------KLYAD--DSAPALAIKAT 45
>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling
proteins; 1.15A {Saccharomyces cerevisiae} SCOP:
d.15.1.1 PDB: 2bwe_S
Length = 77
Score = 42.6 bits (101), Expect = 1e-05
Identities = 17/70 (24%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
+ +K G++ +EV+V + + FK + + G+ + Q+++ G LK+D+ +++ + +
Sbjct: 7 IHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQD 66
Query: 73 GSMVLLMGSK 82
G V L+ S+
Sbjct: 67 GHSVHLVKSQ 76
>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats,
UBL conjugation pathway, nucleus, phosphoprotein; HET:
1PE; 2.40A {Saccharomyces cerevisiae}
Length = 101
Score = 42.3 bits (100), Expect = 2e-05
Identities = 17/70 (24%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
+ +K G++ +EV+V + + FK + + G+ + Q+++ G LK+D+ +++ + +
Sbjct: 31 IHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQD 90
Query: 73 GSMVLLMGSK 82
G V L+ S+
Sbjct: 91 GHSVHLVKSQ 100
>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta,
structural genomics, protein structure initiative; NMR
{Arabidopsis thaliana}
Length = 94
Score = 38.9 bits (91), Expect = 3e-04
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDEW--DNFKLS 71
V VK+ + F V+VD E K +++ + I R ++ G L +D + + ++
Sbjct: 18 VTVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGIT 77
Query: 72 NGSMVLLMGSK 82
S +++
Sbjct: 78 EFSEIVVFLKS 88
>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1
Length = 96
Score = 38.5 bits (90), Expect = 5e-04
Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 1/67 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
V VK ++ E + + FK Q+ + DR ++ G L++ + + +
Sbjct: 20 VSVKTPQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILD 79
Query: 73 GSMVLLM 79
GS V ++
Sbjct: 80 GSTVHVV 86
>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL
conjugation pathway, DNA damage, nucleus,
phosphoprotein; HET: 1PE; 2.40A {Saccharomyces
cerevisiae}
Length = 106
Score = 38.5 bits (90), Expect = 6e-04
Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 14 VKVK-WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLS 71
+ K + KE +D++ + K +L + + + K++ G L++ + L
Sbjct: 4 LTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLK 63
Query: 72 NGSMVLLMGSK 82
+G V+ M S+
Sbjct: 64 DGDQVVFMVSQ 74
>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin,
ubiquitin-like domain, structural genomics, signaling
protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1
Length = 100
Score = 36.9 bits (86), Expect = 0.002
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
V VK K+ + V K ++ + D+ ++ G LK+ + + +
Sbjct: 25 VTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRD 84
Query: 73 GSMVLLM 79
G V L+
Sbjct: 85 GLTVHLV 91
>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein
structur initiative, northeast structural genomics
consortium, NESG; NMR {Homo sapiens}
Length = 101
Score = 36.2 bits (84), Expect = 0.004
Identities = 14/56 (25%), Positives = 23/56 (41%)
Query: 9 PHTYIVKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE 64
P V VK KE E V + FK ++ + D+ ++ G LK+ +
Sbjct: 23 PKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQD 78
>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
unknown function; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 106
Score = 35.8 bits (83), Expect = 0.005
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 1/75 (1%)
Query: 6 GKPPHTYIVKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE- 64
+ PH V VK K+ + V K ++ + D+ ++ G LK+ +
Sbjct: 12 VQDPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDS 71
Query: 65 WDNFKLSNGSMVLLM 79
+ +G V L+
Sbjct: 72 LAQCGVRDGLTVHLV 86
>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural
genomics; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 125
Score = 36.0 bits (83), Expect = 0.007
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 8 PPHTYIVKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WD 66
P V VK KE E V + FK + + Q D+ ++ G LK+ +
Sbjct: 29 EPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLI 88
Query: 67 NFKLSNGSMVLLMGSKEEDSMKEP 90
+ +G V L+ ++ +S
Sbjct: 89 QHGIHDGLTVHLVIKRDPNSSSVD 112
>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1
Length = 102
Score = 35.3 bits (81), Expect = 0.009
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 21 ETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDEW--DNFKLSNGSMVLL 78
TF + V+ D E F+ +GV + +++ L +D ++ L +G MV+L
Sbjct: 22 VTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVL 81
Query: 79 M 79
+
Sbjct: 82 L 82
>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold,
GP78-binding, chaperone; 1.30A {Homo sapiens}
Length = 88
Score = 33.4 bits (77), Expect = 0.026
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE 64
VK + T V FK + + ++Q+++ +G L++D+
Sbjct: 22 VKTLDSQ-TRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDK 71
>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken
structural genomics/proteomics initiative, RSGI, gene
regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB:
1zkh_A
Length = 115
Score = 34.0 bits (78), Expect = 0.027
Identities = 9/45 (20%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G+ + ++ + K +++E TG+ +QK+ +G +K+
Sbjct: 45 GQ-GLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDS 88
>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1
Length = 111
Score = 34.0 bits (78), Expect = 0.028
Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 4/77 (5%)
Query: 7 KPPHTYIVKVK--WGKETFEVDVDTDEEPML-FKAQLYELTGVQIDRQKVMCKGATLKND 63
P T V + E+ V + E + K ++ + ++QK+ K LK++
Sbjct: 25 PGPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDN 84
Query: 64 E-WDNFKLSNGSMVLLM 79
++ + G ++ L
Sbjct: 85 MSLAHYNVGAGEILTLS 101
>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3
protein, PF00240, structural GEN joint center for
structural genomics, JCSG; 1.80A {Homo sapiens} PDB:
1wx9_A
Length = 90
Score = 32.6 bits (75), Expect = 0.061
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE 64
VK + T V FK + + ++Q+++ +G L++D+
Sbjct: 10 VKTLDSQ-TRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDK 59
>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 100
Score = 32.8 bits (74), Expect = 0.067
Identities = 7/83 (8%), Positives = 23/83 (27%), Gaps = 2/83 (2%)
Query: 5 KGKPPHTYIVKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMC--KGATLKN 62
G +V++ +V ++ K L + + + + G +
Sbjct: 3 SGSSGRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDS 62
Query: 63 DEWDNFKLSNGSMVLLMGSKEED 85
+ L + + ++
Sbjct: 63 TVLKSLHLPKNNSLYVLTPDLPP 85
>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding
protein, DNA excision repair, proteasomal degrad
polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U
1p1a_A
Length = 85
Score = 30.3 bits (69), Expect = 0.28
Identities = 15/74 (20%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 14 VKVK-WGKETFEVDVDTDEEPMLFKAQLYELTGVQI---DRQKVMCKGATLKNDE-WDNF 68
+ +K ++TF++ ++ DE + K ++ G QK++ G L +D ++
Sbjct: 8 ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 69 KLSNGSMVLLMGSK 82
++ + V++M +K
Sbjct: 68 RIDEKNFVVVMVTK 81
>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 95
Score = 30.4 bits (69), Expect = 0.35
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 14 VKVK-WGKETFEVDVDTDEEPMLFKAQLYELTGVQI---DRQKVMCKGATLKNDE-WDNF 68
V +K ++TF++D+D +E K ++ G QK++ G L +D +
Sbjct: 3 VTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY 62
Query: 69 KLSNGSMVLLMGSK 82
K+ + V++M +K
Sbjct: 63 KIDEKNFVVVMVTK 76
>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing,
protein binding; 2.60A {Homo sapiens}
Length = 111
Score = 30.6 bits (69), Expect = 0.43
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 6 GKPPHTYIVKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G + VK GK T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 30 GDELLAMQIFVKTLTGK-TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 88
>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase,
deamidati bacterial effector, cell cycle-protein
binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B
Length = 88
Score = 29.6 bits (67), Expect = 0.62
Identities = 15/67 (22%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
VK GK E+D++ ++ K ++ E G+ +Q+++ G + +++ ++K+
Sbjct: 5 VKTLTGK-EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILG 63
Query: 73 GSMVLLM 79
GS++ L+
Sbjct: 64 GSVLHLV 70
>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond,
metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B
2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A
2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A
1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...
Length = 76
Score = 28.8 bits (65), Expect = 0.78
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 14 VKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
+ VK GK T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 3 IFVKTLTGK-TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 53
>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding,
isopeptide BO ligase, nucleotide-binding, UBL
conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A
2kx0_A
Length = 96
Score = 29.3 bits (66), Expect = 0.89
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 14 VKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
+ VK GK T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 4 IFVKTLTGK-TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 54
>3hx8_A MLR2180 protein, putative ketosteroid isomerase; structural
genomics, joint center for structural genomics, JCSG,
protein structure initiative; HET: MSE UNL PG4; 1.45A
{Mesorhizobium loti}
Length = 129
Score = 29.6 bits (66), Expect = 1.1
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 4/68 (5%)
Query: 488 DRIQDFGVKSTEFQSRGQGSSPGRVDIGSN---NSGYYTLQAVLTHKGRTSSSGHYVA-W 543
IQ + + + V + SG ++L+A ++G YV W
Sbjct: 49 QNIQKLWQGAMDMGISELKLTTLDVQESGDFAFESGSFSLKAPGKDSKLVDAAGKYVVVW 108
Query: 544 VKKPNGTW 551
K +G W
Sbjct: 109 RKGQDGGW 116
>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein;
ubiquitin-like domain, solution structure, signaling
protein; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 106
Score = 28.9 bits (65), Expect = 1.2
Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 14 VKVKWGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSN 72
+++ GK ++ V + + K +L+ GV+ Q+ G L + ++ K+
Sbjct: 28 LRLSTGK-DLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPK 86
Query: 73 GSMVLLM 79
+V ++
Sbjct: 87 DYVVQVI 93
>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL
conjugation pathway, ATP-binding, ligase, nucleotide-
binding, polymorphism; 2.85A {Homo sapiens} SCOP:
k.45.1.1 PDB: 3dbr_I 3dbl_I
Length = 88
Score = 28.9 bits (65), Expect = 1.3
Identities = 9/45 (20%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
GK E+D++ ++ K ++ E G+ +Q+++ G + ++
Sbjct: 22 GK-EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDE 65
>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP:
d.15.1.1 PDB: 1yx6_B
Length = 98
Score = 28.6 bits (64), Expect = 1.5
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 14 VKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
+ VK GK T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 3 IFVKTLTGK-TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 53
>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis,
signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1
PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B
2nvu_I* 3dqv_A 1bt0_A
Length = 76
Score = 28.0 bits (63), Expect = 1.6
Identities = 13/62 (20%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE-WDNFKLSNGSMVL 77
GK E+D++ ++ K ++ E G+ +Q+++ G + +++ ++K+ GS++
Sbjct: 10 GK-EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLH 68
Query: 78 LM 79
L+
Sbjct: 69 LV 70
>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon,
inhibitor, ubiqu acetylation, cytoplasm, isopeptide
bond, nucleus; 2.60A {Homo sapiens}
Length = 85
Score = 28.5 bits (64), Expect = 1.6
Identities = 10/45 (22%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G+ T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 13 GR-TIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 56
>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion
protein; ubiquitin interacting motif, UIM, protein
domain interface; NMR {Saccharomyces cerevisiae}
Length = 114
Score = 29.0 bits (65), Expect = 1.7
Identities = 10/45 (22%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
GK T ++V++ + K+++ + G+ D+Q+++ G L++
Sbjct: 19 GK-TITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDG 62
>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific
protease activity, hydrolase, ubiquitin B structural
genomics consortium, SGC; 2.70A {Homo sapiens}
Length = 85
Score = 28.1 bits (63), Expect = 2.0
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 14 VKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
+ VK GK T ++V+ + KA++ + G+ D+Q+++ G L++
Sbjct: 6 IFVKTLTGK-TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 56
>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 81
Score = 28.0 bits (63), Expect = 2.1
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 19 GKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G+ + V DE K + E V + +Q+++ KG L +
Sbjct: 17 GR-ECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADG 60
>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G*
2noq_F 1s1h_G 3iz6_F
Length = 225
Score = 29.0 bits (65), Expect = 2.1
Identities = 4/53 (7%), Positives = 11/53 (20%), Gaps = 3/53 (5%)
Query: 14 VKVK--WGKETFEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKNDE 64
+ V+ +L E+ Q + + +
Sbjct: 3 DTEAPVEVQ-EDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVK 54
>3k5w_A Carbohydrate kinase; 11206B,helicobacter pylori,PSI-II, NYSGXRC, ,
structural genomics, protein structure initiative; 2.60A
{Helicobacter pylori}
Length = 475
Score = 30.2 bits (69), Expect = 2.2
Identities = 7/39 (17%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 97 VEDMNESERAV-SLDLPAGLNNLGNTCYMNAVIQCLKTV 134
E +++ R + D+P+G+++ G + T+
Sbjct: 138 FESLSQKARFKIACDIPSGIDSKGRV--DKRAFKADLTI 174
>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair,
proteasome-mediated degradation, protein- protein
interaction, replication; NMR {Homo sapiens} SCOP:
a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A
Length = 368
Score = 29.2 bits (64), Expect = 3.6
Identities = 15/86 (17%), Positives = 39/86 (45%), Gaps = 5/86 (5%)
Query: 14 VKVK-WGKETFEVDVDTDEEPMLFKAQLYELTGVQ---IDRQKVMCKGATLKNDE-WDNF 68
+ +K ++TF++ ++ DE + K ++ G + QK++ G L +D ++
Sbjct: 10 ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 69
Query: 69 KLSNGSMVLLMGSKEEDSMKEPVVKP 94
++ + V++M +K +
Sbjct: 70 RIDEKNFVVVMVTKTKAGQGTSAPPE 95
>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell
cycle, DNA damage, DNA repair, DNA-binding, ligase, Met
binding, nuclear protein; 2.00A {Homo sapiens} SCOP:
d.15.1.1
Length = 78
Score = 26.9 bits (60), Expect = 3.9
Identities = 7/46 (15%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 19 GKET-FEVDVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G++T + + + ++ EL V+ Q++ +G +++
Sbjct: 12 GRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDG 57
>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain,
NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.15.1.1
Length = 89
Score = 27.0 bits (60), Expect = 5.5
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 19 GKETFEV-DVDTDEEPMLFKAQLYELTGVQIDRQKVMCKGATLKND 63
G +T + DV + +++ L V+ + Q++ +G L+N
Sbjct: 17 GSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENG 62
>3u24_A Putative lipoprotein; COG4805, DUF885, structural genomics,
PSI-biology, midwest C structural genomics, MCSG, lipid
BIND protein; 2.25A {Shewanella oneidensis}
Length = 572
Score = 28.8 bits (64), Expect = 6.1
Identities = 17/150 (11%), Positives = 40/150 (26%), Gaps = 20/150 (13%)
Query: 408 KEKERINA---KVLKDIKFPIEFDAYELCTPE-LQAKLAPMREKFKIAEE---------K 454
+K+R+ K+ + ++ + + K ++
Sbjct: 269 VDKDRVQGEMAKITDKLWPKYFTTPKPSDNKIAIRQLIDKLSTKHVKRDDFVSEVRKQIP 328
Query: 455 EAFEEFRTQYVFISIPMDEIYVRFGQKIYAPV--GDRIQDFGVKSTEFQSRG--QGSSPG 510
E E + + P + VR + + + + G S
Sbjct: 329 ELIEFVNQKNIVTLDPKKPLVVRETPEYMRGYASISAPGPYDKLGNTYYNVTPLDGMSNE 388
Query: 511 RVDIGSNNSGYYTLQAVLTHKGRTSSSGHY 540
+ ++ LQ + H+ GHY
Sbjct: 389 SAESYLREYNHWILQILNIHEA---IPGHY 415
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.134 0.391
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,530,290
Number of extensions: 499799
Number of successful extensions: 1232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1177
Number of HSP's successfully gapped: 84
Length of query: 577
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 478
Effective length of database: 3,937,614
Effective search space: 1882179492
Effective search space used: 1882179492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.9 bits)