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= 003533
(812 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 621 bits (1602), Expect = e-178, Method: Compositional matrix adjust.
Identities = 342/742 (46%), Positives = 459/742 (61%), Gaps = 39/742 (5%)
Query: 7 LRSNLSRVRIPEPTNRIFKQECCVSFDTPRSEGGLFVDLNSFLAYGKDHVGWNFEKTGNP 66
L S L +R+P+ +R+ K EC SFDTP SEGGL++ +N+FL +GK +V +F KTG
Sbjct: 28 LLSVLPTIRVPKAGDRVHKDECAFSFDTPESEGGLYICMNTFLGFGKQYVERHFNKTGQR 87
Query: 67 VYLHIKQTRK------LVAPEDRPSKKPTLLAIGVEGGFDNNEAEY--DETHSIVILPEY 118
VYLH+++TR+ D P KKPT LAIGVEGGFD +E ++ DE IVILP+Y
Sbjct: 88 VYLHLRRTRRPKEEDPATGTGDPPRKKPTRLAIGVEGGFDLSEEKFELDEDVKIVILPDY 147
Query: 119 VTLSYPSVE-LPEKVR----LAVDAILMAEGAERKEQVAAWTADKKQTSAYAMNLQQIDN 173
+ ++ + LP+ VR AV+A+L A+ A RK++V AW + +Q S +A +L+Q+DN
Sbjct: 148 LEIARDGLGGLPDIVRDRVTSAVEALLSADSASRKQEVQAWDGEVRQVSKHAFSLKQLDN 207
Query: 174 GVIIPPSGWKCAKCDKRDNLWLNLTDGMILCGRRNWDGTGGNNHAVEHYKETGYPLAVKL 233
IPP GWKC+KCD R+NLWLNLTDG ILCGRR +DG+GGNNHAVEHY+ETGYPLAVKL
Sbjct: 208 PARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKL 267
Query: 234 GTITSDLEGADVFSYPEDDSVVDPLLAQHLAFFGIDFSSLQKTEMTTAERELDQNTNF-D 292
GTIT D GADV+SY EDD V+DP LA+HL+ FGID +QKT+ T E E+D N +
Sbjct: 268 GTITPD--GADVYSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTDKTMTELEIDMNQRIGE 325
Query: 293 WNRIQESGQDVEPLFGPGYTGLVNLGNSCYLAATMQVMFSTHAFCTRYYTQEPLKAAFEA 352
W IQESG ++PLFGPGYTG+ NLGNSCYL + +QV+FS F +Y + L+ F+
Sbjct: 326 WELIQESGVPLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDK--LEKIFQN 383
Query: 353 APADPTVDLNMQLTKLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAA 412
AP DPT D + Q+ KL HGLLSG+YS P E Q+GI PRMFKA+I
Sbjct: 384 APTDPTQDFSTQVAKLGHGLLSGEYSKPVPESGDGERVPEQKEV-QDGIAPRMFKALIGK 442
Query: 413 SHPEFSSMRQQDALEFFLHFVDQVERVHSGKPEVDPTKSFKFGIEERISC-PSGKVAYNR 471
HPEFS+ RQQDA EFFLH ++ VER + + +P + F+F +EE+I C + KV Y +
Sbjct: 443 GHPEFSTNRQQDAQEFFLHLINMVER--NCRSSENPNEVFRFLVEEKIKCLATEKVKYTQ 500
Query: 472 RLDYILSLGIPLDEATNKEELAAFQKLKMERISEGKDVTNEEIVRPRVPLEACLSTFSAP 531
R+DYI+ L +P+D A NKEEL + +R +E + + E+VR +VP +CL + AP
Sbjct: 501 RVDYIMQLPVPMDAALNKEELLE--YEEKKRQAEEEKMALPELVRAQVPFSSCLEAYGAP 558
Query: 532 EELPDFYXXXXXXXXXXXXXXXXXXFPDYLVLHMRKFVMEAGWVPKKLXXXXXXXXXXXX 591
E++ DF+ FPDYLV+ ++KF WVPKKL
Sbjct: 559 EQVDDFWSTALQAKSVAVKTTRFASFPDYLVIQIKKFTFGLDWVPKKLDVSIEMPEELDI 618
Query: 592 SHMRSKXXXXXXXXXXXXX----XXDEVQSNKPVANKDIVSQLVSMGFNHLHCEKAAVNT 647
S +R DE ++ P+ ++ ++ QLV MGF C KA T
Sbjct: 619 SQLRGTGLQPGEEELPDIAPPLVTPDEPKA--PMLDESVIIQLVEMGFPMDACRKAVYYT 676
Query: 648 SNAGVEEAMNWLLSHMDDPDIDMPL------SQETQCAAID---QSKVETLLSFGFSEEV 698
N+G E AMNW++SHMDDPD PL + AA D + V T++S GFS +
Sbjct: 677 GNSGAEAAMNWVMSHMDDPDFANPLILPGSSGPGSTSAAADPPPEDCVTTIVSMGFSRDQ 736
Query: 699 ARNALKASGGDIEKATDWIFNN 720
A AL+A+ +E+A DWIF++
Sbjct: 737 ALKALRATNNSLERAVDWIFSH 758
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 624 KDIVSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLSQETQCAAID 682
+D V+ +VSMGF+ KA T+N+ +E A++W+ SH+DD D + + +A D
Sbjct: 721 EDCVTTIVSMGFSRDQALKALRATNNS-LERAVDWIFSHIDDLDAEAAMDISEGRSAAD 778
>pdb|2G43|A Chain A, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G43|B Chain B, Structure Of The Znf Ubp Domain From Deubiquitinating
Enzyme Isopeptidase T (Isot)
pdb|2G45|A Chain A, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
pdb|2G45|D Chain D, Co-Crystal Structure Of Znf Ubp Domain From The
Deubiquitinating Enzyme Isopeptidase T (Isot) In Complex
With Ubiquitin
Length = 129
Score = 189 bits (481), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 87/130 (66%), Positives = 106/130 (81%), Gaps = 2/130 (1%)
Query: 148 KEQVAAWTADKKQTSAYAMNLQQIDNGVIIPPSGWKCAKCDKRDNLWLNLTDGMILCGRR 207
K++V AW + +Q S +A +L+Q+DN IPP GWKC+KCD R+NLWLNLTDG ILCGRR
Sbjct: 1 KQEVQAWDGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRR 60
Query: 208 NWDGTGGNNHAVEHYKETGYPLAVKLGTITSDLEGADVFSYPEDDSVVDPLLAQHLAFFG 267
+DG+GGNNHAVEHY+ETGYPLAVKLGTIT D GADV+SY EDD V+DP LA+HL+ FG
Sbjct: 61 YFDGSGGNNHAVEHYRETGYPLAVKLGTITPD--GADVYSYDEDDMVLDPSLAEHLSHFG 118
Query: 268 IDFSSLQKTE 277
ID +QKT+
Sbjct: 119 IDMLKMQKTD 128
>pdb|2L80|A Chain A, Solution Structure Of The Zinc Finger Domain Of Usp13
Length = 116
Score = 161 bits (407), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 75/117 (64%), Positives = 92/117 (78%), Gaps = 2/117 (1%)
Query: 160 QTSAYAMNLQQIDNGVIIPPSGWKCAKCDKRDNLWLNLTDGMILCGRRNWDGTGGNNHAV 219
S YA NL Q+DNGV IPPSGWKCA+CD R+NLWLNLTDG +LCG+ +D +GGN HA+
Sbjct: 2 SVSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHAL 61
Query: 220 EHYKETGYPLAVKLGTITSDLEGADVFSYPEDDSVVDPLLAQHLAFFGIDFSSLQKT 276
EHY++ GYPLAVKLGTIT D GADV+S+ E++ V+DP LA+HLA FGID + T
Sbjct: 62 EHYRDMGYPLAVKLGTITPD--GADVYSFQEEEPVLDPHLAKHLAHFGIDMLHMHGT 116
>pdb|1VEK|A Chain A, Solution Structure Of Rsgi Ruh-011, A Uba Domain From
Arabidopsis Cdna
Length = 84
Score = 104 bits (260), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 46/59 (77%), Positives = 56/59 (94%)
Query: 615 VQSNKPVANKDIVSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLS 673
++S +PVAN++IV+QLVSMGF+ LHC+KAA+NTSNAGVEEAMNWLLSHMDDPDID P+S
Sbjct: 21 MESAQPVANEEIVAQLVSMGFSQLHCQKAAINTSNAGVEEAMNWLLSHMDDPDIDAPIS 79
>pdb|1WIV|A Chain A, Solution Structure Of Rsgi Ruh-023, A Uba Domain From
Arabidopsis Cdna
Length = 73
Score = 95.9 bits (237), Expect = 8e-20, Method: Composition-based stats.
Identities = 45/59 (76%), Positives = 52/59 (88%), Gaps = 2/59 (3%)
Query: 662 HMDDPDIDMPLSQETQCAAIDQSKVETLLSFGFSEEVARNALKASGGDIEKATDWIFNN 720
HMDDPDID P+S +T + IDQS V+TLLSFGF+E+VAR ALKASGGDIEKATDW+FNN
Sbjct: 11 HMDDPDIDAPISHQT--SDIDQSSVDTLLSFGFAEDVARKALKASGGDIEKATDWVFNN 67
>pdb|2LBC|A Chain A, Solution Structure Of Tandem Uba Of Usp13
Length = 126
Score = 66.6 bits (161), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 38/111 (34%), Positives = 54/111 (48%), Gaps = 16/111 (14%)
Query: 627 VSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLSQETQ--------- 677
V QL MGF C KA T N G E A NW++ HM++PD PL+
Sbjct: 7 VMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGAS 66
Query: 678 ---CAAID----QSKVETLLSFGFSEEVARNALKASGGDIEKATDWIFNNP 721
+ +D + V + S GF A AL+A+ ++E+A DWIF++P
Sbjct: 67 VFGASGLDNQPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHP 117
>pdb|2DAG|A Chain A, Solution Structure Of The First Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 74
Score = 60.8 bits (146), Expect = 3e-09, Method: Composition-based stats.
Identities = 26/50 (52%), Positives = 33/50 (66%)
Query: 623 NKDIVSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPL 672
++ ++ QLV MGF C KA T N+G E AMNW++SHMDDPD PL
Sbjct: 9 DESVIIQLVEMGFPMDACRKAVYYTGNSGAEAAMNWVMSHMDDPDFANPL 58
>pdb|1WHC|A Chain A, Solution Structure Of Rsgi Ruh-027, A Uba Domain From
Mouse Cdna
Length = 64
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/47 (51%), Positives = 30/47 (63%)
Query: 627 VSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLS 673
+ L+ MGF EKA T N G+E AM+WL+ H DDPD+D PLS
Sbjct: 13 LESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLS 59
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 58/289 (20%), Positives = 107/289 (37%), Gaps = 40/289 (13%)
Query: 301 QDVEPLFG---PGYTGLVNLGNSCYLAATMQVMFS----THAFCTRYYTQEPLKAAFEAA 353
+++ P+FG P TGL NLGN+CY+ + +Q + + F Y + ++
Sbjct: 49 RNLNPVFGGSGPALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGH 108
Query: 354 PADPTVDLNMQLTKLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAAS 413
+ + + + L +G+Y I P+ FK I
Sbjct: 109 KGEVAEEFGI----IMKALWTGQYRY---------------------ISPKDFKITIGKI 143
Query: 414 HPEFSSMRQQDALEFFLHFVDQVERVHSGKPEVDPTKSFKFGIEERI-SCPSGKVAYNRR 472
+ +F+ QQD+ E L +D +H + D K +K + + + + A+ +
Sbjct: 144 NDQFAGYSQQDSQELLLFLMDG---LHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKH 200
Query: 473 LDYILSLGIPLDEATNKEELAAFQKLKMERISEGKDVTNEEIVR-PRVPLEACLSTFSAP 531
S+ + L + K + K R E + + + L+ CL FS
Sbjct: 201 KQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKE 260
Query: 532 EELPD---FYXXXXXXXXXXXXXXXXXXFPDYLVLHMRKFVMEAGWVPK 577
E+L D FY P L++H+++F + W K
Sbjct: 261 EKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQK 309
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 58/289 (20%), Positives = 105/289 (36%), Gaps = 40/289 (13%)
Query: 301 QDVEPLFG---PGYTGLVNLGNSCYLAATMQVMFS----THAFCTRYYTQEPLKAAFEAA 353
+++ P+FG P TGL NLGN+CY + +Q + + F Y + ++
Sbjct: 49 RNLNPVFGGSGPALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGH 108
Query: 354 PADPTVDLNMQLTKLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAAS 413
+ + + + L +G+Y I P+ FK I
Sbjct: 109 KGEVAEEFGI----IXKALWTGQYRY---------------------ISPKDFKITIGKI 143
Query: 414 HPEFSSMRQQDALEFFLHFVDQVERVHSGKPEVDPTKSFKFGIEERI-SCPSGKVAYNRR 472
+ +F+ QQD+ E L D +H + D K +K + + + + A+ +
Sbjct: 144 NDQFAGYSQQDSQELLLFLXDG---LHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKH 200
Query: 473 LDYILSLGIPLDEATNKEELAAFQKLKMERISEGKDVTNEEIVR-PRVPLEACLSTFSAP 531
S+ + L + K + K R E + + + L+ CL FS
Sbjct: 201 KQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLFSKE 260
Query: 532 EELPD---FYXXXXXXXXXXXXXXXXXXFPDYLVLHMRKFVMEAGWVPK 577
E+L D FY P L++H+++F + W K
Sbjct: 261 EKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQK 309
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 63/303 (20%), Positives = 111/303 (36%), Gaps = 70/303 (23%)
Query: 309 PGYTGLVNLGNSCYLAATMQVMFSTHAFCTRYYTQEPLKAAFEAAPADPTVDLNMQLTKL 368
PG GL NLGN+ ++ + +Q + +T A T Y+ ++ +A D + + ++ +
Sbjct: 6 PGLCGLGNLGNTXFMNSALQCLSNT-APLTDYFLKDEYEAEINR---DNPLGMKGEIAEA 61
Query: 369 AHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAASHPEFSSMRQQDALEF 428
L+ +S + + PRMFK + P+FS +QQD+ E
Sbjct: 62 YAELIKQMWS-----------------GRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQEL 104
Query: 429 FLHFVD----QVERVH----------SGKPEVDPTK----------------SFKFGIEE 458
+D + RV +G+P+ K +F +
Sbjct: 105 LAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKS 164
Query: 459 RISCPS-GKVAYNRRLDYILSLGIPLDEATNKEELAAFQKLKMERISEGKDVTNEEIVRP 517
+ CP KV+ D L +PL LK +R+ EG + ++ +
Sbjct: 165 TLVCPECAKVSVT--FDPFCYLTLPL-------------PLKKDRVMEGPMLQPQKKKKT 209
Query: 518 RVPLEACLSTFSAPEELPD---FYXXXXXXXXXXXXXXXXXXFPDYLVLHMRKFVMEAGW 574
V L C+ F+ E L + +Y P LV+H+++F W
Sbjct: 210 TVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYW 269
Query: 575 VPK 577
K
Sbjct: 270 RDK 272
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 56/138 (40%), Gaps = 32/138 (23%)
Query: 306 LFGPGYTGLVNLGNSCYLAATMQVMFSTHA---FCTRYYTQEPLKAAFEAAPADPTVDLN 362
L G G+ GL NLGN+C+L A +Q + ST FC R ++ + A
Sbjct: 11 LLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRA---------- 60
Query: 363 MQLTKLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAASHPEFSSMRQ 422
+LT+ ++ + + E + P F+AV P FS Q
Sbjct: 61 QELTEAFADVIGALWHPDS----------------CEAVNPTRFRAVFQKYVPSFSGYSQ 104
Query: 423 QDALEFFLHFVDQVERVH 440
QDA EF +ER+H
Sbjct: 105 QDAQEFLKLL---MERLH 119
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/139 (26%), Positives = 55/139 (39%), Gaps = 32/139 (23%)
Query: 305 PLFGPGYTGLVNLGNSCYLAATMQVMFSTHA---FCTRYYTQEPLKAAFEAAPADPTVDL 361
P G+ GL NLGN+C+L A +Q + ST FC R ++ + A
Sbjct: 16 PRGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRA--------- 66
Query: 362 NMQLTKLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAASHPEFSSMR 421
+LT+ ++ + + E + P F+AV P FS
Sbjct: 67 -QELTEAFADVIGALWHPDS----------------CEAVNPTRFRAVFQKYVPSFSGYS 109
Query: 422 QQDALEFFLHFVDQVERVH 440
QQDA EF +ER+H
Sbjct: 110 QQDAQEFLKLL---MERLH 125
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/134 (26%), Positives = 54/134 (40%), Gaps = 32/134 (23%)
Query: 310 GYTGLVNLGNSCYLAATMQVMFSTHA---FCTRYYTQEPLKAAFEAAPADPTVDLNMQLT 366
G+ GL NLGN+C+L A +Q + ST FC R ++ + A +LT
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRA----------QELT 51
Query: 367 KLAHGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAASHPEFSSMRQQDAL 426
+ ++ + + E + P F+AV P FS QQDA
Sbjct: 52 EAFADVIGALWHPDS----------------CEAVNPTRFRAVFQKYVPSFSGYSQQDAQ 95
Query: 427 EFFLHFVDQVERVH 440
EF +ER+H
Sbjct: 96 EFLKLL---MERLH 106
>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 63
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 624 KDIVSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLS 673
+D V+ +VSMGF+ KA T+N+ +E A++W+ SH+DD D + +S
Sbjct: 10 EDCVTTIVSMGFSRDQALKALRATNNS-LERAVDWIFSHIDDLDAEAAMS 58
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 25/35 (71%)
Query: 686 VETLLSFGFSEEVARNALKASGGDIEKATDWIFNN 720
V T++S GFS + A AL+A+ +E+A DWIF++
Sbjct: 13 VTTIVSMGFSRDQALKALRATNNSLERAVDWIFSH 47
>pdb|2DAI|A Chain A, Solution Structure Of The First Uba Domain In The Human
Ubiquitin Associated Domain Containing 1 (Ubadc1)
Length = 83
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 627 VSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLS 673
+ QL MGF KA + ++ V +AM WL+ H +DP ID PLS
Sbjct: 33 LRQLTEMGFPENRATKA-LQLNHMSVPQAMEWLIEHAEDPTIDTPLS 78
>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 = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 50/275 (18%), Positives = 89/275 (32%), Gaps = 60/275 (21%)
Query: 310 GYTGLVNLGNSCYLAATMQVMFSTHAFCTRYYTQEPLKAAFEAAPADPTVDLNMQLTKLA 369
G +GL+N+GN+C++++ +Q + F +Q + P + L K+
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQ---IHSNNCKVRSPDKCFSCALDKIV 196
Query: 370 HGLLSGKYSVPAQEKXXXXXXXXXXXXKQEGIPPRMFKAVIAASHPEFSSMRQQDALEFF 429
H L + A +Q G + A + + QQDA EF+
Sbjct: 197 HELYGALNTKQASSS-------STSTNRQTGFIYLLTCA--WKINQNLAGYSQQDAHEFW 247
Query: 430 LHFVDQ--------------VERVHSGKPEVDPTKSFKFGIEERISCPSGKVAYNRRLDY 475
++Q V R ++ + E F+ +E I CP + +D
Sbjct: 248 QFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDP 307
Query: 476 ILSLGIPLDEATNKEELAAFQKLKMERISEGKDVTNEEIVRPRVPLEACLSTFSAPEELP 535
L L + ++ + L CL +F E+L
Sbjct: 308 FLDLSLD--------------------------------IKDKKKLYECLDSFHKKEQLK 335
Query: 536 DF--YXXXXXXXXXXXXXXXXXXFPDYLVLHMRKF 568
DF + P LVL +++F
Sbjct: 336 DFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRF 370
>pdb|2CRN|A Chain A, Solution Structure Of The Uba Domain Of Human Ubash3a
Protein
Length = 64
Score = 36.2 bits (82), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 626 IVSQLVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSHMDDPDIDMPLS 673
++ L++MGF KA T EEA+ WL H +DP +D P+S
Sbjct: 12 LLEPLLAMGFPVHTALKALAATGRKTAEEALAWLHDHCNDPSLDDPIS 59
>pdb|2CPW|A Chain A, Solution Structure Of Rsgi Ruh-031, A Uba Domain From
Human Cdna
Length = 64
Score = 34.3 bits (77), Expect = 0.31, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 684 SKVETLLSFGFSEEVARNALKASGG-DIEKATDWIFNN 720
S ++ LLS GF A+ AL ++GG ++ A DW+F++
Sbjct: 21 SALDVLLSMGFPRARAQKALASTGGRSVQTACDWLFSH 58
Score = 32.7 bits (73), Expect = 0.75, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 630 LVSMGFNHLHCEKAAVNTSNAGVEEAMNWLLSH 662
L+SMGF +KA +T V+ A +WL SH
Sbjct: 26 LLSMGFPRARAQKALASTGGRSVQTACDWLFSH 58
>pdb|4AE4|A Chain A, The Ubap1 Subunit Of Escrt-I Interacts With Ubiquitin Via
A Novel Souba Domain
pdb|4AE4|B Chain B, The Ubap1 Subunit Of Escrt-I Interacts With Ubiquitin Via
A Novel Souba Domain
Length = 118
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 675 ETQCAAIDQSKVETLLSFGFSEEVARNALKASGGDIEKATDWIF 718
E QC VET+++ G+S E A KA+G +IE+ D++F
Sbjct: 8 ERQC-------VETVVNXGYSYECVLRAXKAAGANIEQILDYLF 44
>pdb|1WGN|A Chain A, Solution Structure Of Uba Domain Of Human Ubiquitin
Associated Protein 1 (Ubap1)
Length = 63
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 667 DIDMPLSQETQCAAIDQSKVETLLSFGFSEEVARNALKASGGDIEKATDWIF 718
++ M E QC VET+++ G+S E A+K G +IE+ D++F
Sbjct: 11 ELQMLSPSERQC-------VETVVNMGYSYECVLRAMKKKGENIEQILDYLF 55
>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 = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 313 GLVNLGNSCYLAATMQVMFS 332
GL NLGN+CY+ AT+Q + S
Sbjct: 16 GLTNLGNTCYMNATVQCIRS 35
>pdb|2G3Q|A Chain A, Solution Structure Of Ede1 Uba-Ubiquitin Complex
Length = 43
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 686 VETLLSFGFSEEVARNALKASGGDIEKATDWIFNN 720
VE L GF+EE A NAL+ D+E AT+++ ++
Sbjct: 8 VEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS 42
>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 = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 310 GYTGLVNLGNSCYLAATMQVMFSTHAFCTRYY 341
GY GL N G +CY+ + +Q +F T+ Y
Sbjct: 5 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVY 36
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 310 GYTGLVNLGNSCYLAATMQVMFSTHAFCTRYY 341
GY GL N G +CY+ + +Q +F T+ Y
Sbjct: 174 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVY 205
>pdb|2V95|A Chain A, Struture Of Corticosteroid-Binding Globulin In Complex
With Cortisol
Length = 371
Score = 29.3 bits (64), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 25/104 (24%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 249 PEDDSVVDPLLAQHLAFFGIDFSSLQKTEMTTAERELDQNTNFDWNRIQESGQDVEPLFG 308
P+ ++++ P+ + +A + S Q + + L + + + I +S Q + L
Sbjct: 29 PDKNTLISPV-SISMALAMVSLGSAQTQSLQSLGFNLTETSEAE---IHQSFQYLNYLLK 84
Query: 309 PGYTGL-VNLGNSCYLAATMQVMFSTHAFCTRYYTQEPLKAAFE 351
TGL +N+GN+ +L +++ S A +YY E L FE
Sbjct: 85 QSDTGLEMNMGNAMFLLQKLKLKDSFLADVKQYYESEALAIDFE 128
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
0.318 0.135 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,004,025
Number of Sequences: 62578
Number of extensions: 938913
Number of successful extensions: 1818
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1755
Number of HSP's gapped (non-prelim): 44
length of query: 812
length of database: 14,973,337
effective HSP length: 107
effective length of query: 705
effective length of database: 8,277,491
effective search space: 5835631155
effective search space used: 5835631155
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)