RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14778
(210 letters)
>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 = 98.8 bits (246), Expect = 6e-25
Identities = 28/122 (22%), Positives = 45/122 (36%), Gaps = 29/122 (23%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGG 60
MR+ ++ T K+N F FP +L + +++K
Sbjct: 200 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKT-------------------------- 233
Query: 61 EDFNENYEYELIGVTVHTGTADGGHYYSFIRDR--DKWLLFNDAEVKHFDSSQLAAECFG 118
D + Y L V VH+G GGHY ++ + KW F+D V + +G
Sbjct: 234 -DPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYG 292
Query: 119 GE 120
G
Sbjct: 293 GH 294
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 99.3 bits (247), Expect = 2e-24
Identities = 28/122 (22%), Positives = 45/122 (36%), Gaps = 29/122 (23%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGG 60
MR+ ++ T K+N F FP +L + +++K
Sbjct: 369 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKT-------------------------- 402
Query: 61 EDFNENYEYELIGVTVHTGTADGGHYYSFIRDR--DKWLLFNDAEVKHFDSSQLAAECFG 118
D + Y L V VH+G GGHY ++ + KW F+D V + +G
Sbjct: 403 -DPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYG 461
Query: 119 GE 120
G
Sbjct: 462 GH 463
>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 = 92.0 bits (228), Expect = 3e-22
Identities = 27/143 (18%), Positives = 48/143 (33%), Gaps = 23/143 (16%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGG 60
+R+ + + KV FP+ LDM L + + +
Sbjct: 239 VRFFYKEKESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNT 298
Query: 61 EDF---------------------NENYEYELIGVTVHTG-TADGGHYYSFIRDR-DKWL 97
D N Y+L V H G ++ GHY S+++ + D+W+
Sbjct: 299 SDKKSSPQKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWI 358
Query: 98 LFNDAEVKHFDSSQLAAECFGGE 120
F+D +V + GG+
Sbjct: 359 KFDDDKVSIVTPEDILRLSGGGD 381
>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 = 82.7 bits (204), Expect = 8e-19
Identities = 27/117 (23%), Positives = 43/117 (36%), Gaps = 21/117 (17%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGG 60
R+ + K++ FP L+M Y +H + K
Sbjct: 368 KRFEHLL-NGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGK---------------- 410
Query: 61 EDFNENYEYELIGVTVHTGTADGGHYYSFIRDR-DKWLLFNDAEVKHFDSSQLAAEC 116
+ YELIG+ H GT + GHY +F + +W FND+ V ++ E
Sbjct: 411 ---VPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQ 464
>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 = 75.3 bits (184), Expect = 3e-16
Identities = 34/171 (19%), Positives = 57/171 (33%), Gaps = 51/171 (29%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQHYQ------------------- 41
+R+ + T K K+ FP +LD++ + + +
Sbjct: 231 VRFFWKRSTNKKSKILRKVVFPFQLDVADMLTPEYAAEKVKVRDELRKVEKEKNEKEREI 290
Query: 42 ----------------------------EEKLKSEARGEGEVGGEGGEDFNENYEYELIG 73
EK + + + N + Y LIG
Sbjct: 291 KRRKFDPSSSENVMTPREQYETQVALNESEKDQWLEEYKKHFPPNLEKGENPSCVYNLIG 350
Query: 74 VTVHTG-TADGGHYYSFIR---DRDKWLLFNDAEVKHFDSSQLAAECFGGE 120
V H G ++ GHY +FIR D +KW FND +V + ++ + GGE
Sbjct: 351 VITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGE 401
>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 = 63.3 bits (154), Expect = 3e-12
Identities = 27/110 (24%), Positives = 43/110 (39%), Gaps = 32/110 (29%)
Query: 5 FNMVTMLKEKVNTHFSFPMR-LDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGGEDF 63
F+ + K+ T +FP+R LD+ + ++
Sbjct: 248 FSESRIRTSKLTTFVNFPLRDLDLREFASEN----------------------------- 278
Query: 64 NENYEYELIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQ 111
+ Y L V+ H+GT GGHY ++ R +W FND+ V SSQ
Sbjct: 279 TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQ 328
>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 = 63.1 bits (153), Expect = 4e-12
Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 30/109 (27%)
Query: 5 FNMVTMLKEKVNTHFSFPMR-LDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGGEDF 63
F+ +K + FP++ L + + D
Sbjct: 258 FSASRGSIKKSSVGVDFPLQRLSLGDFAS-----------------------------DK 288
Query: 64 NENYEYELIGVTVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQL 112
+ Y+L + H+G+ GHY + R + W ++ND+ V +Q+
Sbjct: 289 AGSPVYQLYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQV 337
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 61.1 bits (148), Expect = 2e-11
Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 31/111 (27%)
Query: 5 FNMVTMLKEKVNTHFSFPMR-LDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGGEDF 63
F+ ++K++T FP+R L+MS +V
Sbjct: 263 FSYNRYWRDKLDTVVEFPIRGLNMSEFVC----------------------------NLS 294
Query: 64 NENYEYELIGVTVHTGTADGGHYYSFIRDR--DKWLLFNDAEVKHFDSSQL 112
Y Y+LI V+ H G GHY ++ +++ KW F+D+ V Q+
Sbjct: 295 ARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQI 345
>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 = 59.5 bits (144), Expect = 9e-11
Identities = 29/111 (26%), Positives = 43/111 (38%), Gaps = 31/111 (27%)
Query: 5 FNMVTMLKEKVNTHFSFPMR-LDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGGEDF 63
F+ K+K+ T FP+ LD+S YV
Sbjct: 300 FSYDGRWKQKLQTSVDFPLENLDLSQYVI----------------------------GPK 331
Query: 64 NENYEYELIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQL 112
N +Y L V+ H G DGGHY ++ ++ R +W F+D EV S +
Sbjct: 332 NNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSV 382
>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 = 58.8 bits (141), Expect = 2e-10
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 10/87 (11%)
Query: 19 FSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARGEGEVGGEGGEDFNENYEYELIGVTVHT 78
FS LD ++ + +S A E G + + +Y+L H
Sbjct: 756 FSHIDDLDAEAAMD---------ISEGRSAADSISESVPVGPKVRDGPGKYQLFAFISHM 806
Query: 79 GT-ADGGHYYSFIRDRDKWLLFNDAEV 104
GT GHY I+ +W+++ND +V
Sbjct: 807 GTSTMCGHYVCHIKKEGRWVIYNDQKV 833
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.39
Identities = 8/54 (14%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 41 QEEKLKSEARGEGEVGGEGGEDFNENYEYELIGVTVHTGTADGGHYYSFIRDRD 94
E++ + +A+ + E++N+ ++ ++ AD +F + D
Sbjct: 108 MEQEWREKAKKD-------LEEWNQRQSEQVEKNKINNRIADK----AFYQQPD 150
Score = 26.7 bits (58), Expect = 4.5
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 9/37 (24%)
Query: 38 QHYQE--EKLKSEARGEGEVGGEGGEDFNENYEYELI 72
Q E EK K R + + F + + ++I
Sbjct: 125 QRQSEQVEKNKINNRIA-D------KAFYQQPDADII 154
>3rza_A Tripeptidase; phosphorylase/hydrolase-like, structural genomics,
joint CEN structural genomics, JCSG, protein structure
initiative; HET: CIT PG4 PGE; 2.10A {Staphylococcus
aureus subsp}
Length = 396
Score = 29.2 bits (66), Expect = 0.92
Identities = 8/35 (22%), Positives = 11/35 (31%), Gaps = 1/35 (2%)
Query: 51 GEGEVGGEGGEDFN-ENYEYELIGVTVHTGTADGG 84
+VG ++IG T H T G
Sbjct: 187 ASADVGTTVVGAPTQMLISAKIIGKTAHASTPKEG 221
>3mit_A Lectin; all beta sheet protein, beta prism-I fold, mannose
specific, binding protein; HET: MAN; 2.32A {Musa
acuminata} PDB: 1x1v_A* 3miu_A* 3miv_A 2bmz_A* 2bmy_A*
2bn0_A*
Length = 141
Score = 27.9 bits (62), Expect = 1.3
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 53 GEVGGEGGEDFNENYEYELIGVTVHTGTA 81
G GG GG F+ Y +I V + +G
Sbjct: 8 GAWGGNGGSAFDMGPAYRIISVKIFSGDV 36
>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 = 28.5 bits (63), Expect = 1.8
Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 31/88 (35%)
Query: 56 GGEGGEDFNENYE---YELIGVTVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQL 112
GGE G+ ENY +E DG + + + +F + + S+
Sbjct: 1677 GGEKGKRIRENYSAMIFE--------TIVDG-------KLKTE-KIFKEI---NEHSTSY 1717
Query: 113 AAECFGGEMTVLNA------CLKLLSTA 134
F E +L+A L L+ A
Sbjct: 1718 ---TFRSEKGLLSATQFTQPALTLMEKA 1742
>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus
thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*
Length = 311
Score = 27.9 bits (63), Expect = 2.3
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 24 RLDMSGYVEKH 34
R+DM+ Y+EKH
Sbjct: 80 RIDMTEYMEKH 90
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A
{Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20
c.37.1.20
Length = 854
Score = 28.3 bits (64), Expect = 2.5
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 24 RLDMSGYVEKH 34
R+DM+ Y+EKH
Sbjct: 621 RIDMTEYMEKH 631
>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 6.93A {Bacillus subtilis}
Length = 758
Score = 27.9 bits (63), Expect = 2.6
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 24 RLDMSGYVEKH 34
R+DMS Y+EKH
Sbjct: 554 RIDMSEYMEKH 564
>1xxq_A Mannose-binding lectin; tetrameric B-prism fold, jacalin-fold,
sugar binding protein; 1.80A {Morus nigra} PDB: 1xxr_A*
1j4t_A 1j4s_A 1j4u_A* 1vbp_A* 1vbo_A*
Length = 161
Score = 26.8 bits (59), Expect = 3.6
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 53 GEVGGEGGEDFNENYEYELIGVTVHTGTADGGHYYSFIRDRD 94
G GG GG +++ + + + G D +S I D +
Sbjct: 20 GLWGGPGGNAWDDGSYTGIREINLSHG--DAIGAFSVIYDLN 59
>2fe8_A PP1AB, ORF1AB, replicase polyprotein 1AB; protease, hydrolase;
1.85A {Sars coronavirus} PDB: 3e9s_A* 3mj5_A*
Length = 315
Score = 27.5 bits (60), Expect = 3.6
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 75 TVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQLAA 114
+TG GH Y+ I ++ + A + +
Sbjct: 263 NEYTGNYQCGH-YTHITAKETLYRIDGAHLTKMSEYKGPV 301
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 27.6 bits (62), Expect = 3.7
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 24 RLDMSGYVEKH 34
R DMS Y+E+H
Sbjct: 518 RFDMSEYMERH 528
>2e60_A SFRS8 protein, splicing factor, arginine/serine-rich 8; SURP
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 101
Score = 25.7 bits (56), Expect = 6.7
Identities = 13/62 (20%), Positives = 19/62 (30%), Gaps = 17/62 (27%)
Query: 5 FNMVTMLKEKVNTHFSFPMRLDMSGYVEKHLMPQH----YQEEKLKSEARGEGEVGGEGG 60
F ++ K+ N+ F F L H Y + K+ G V E
Sbjct: 45 FEIMLKAKQARNSQFDF-------------LRFDHYLNPYYKFIQKAMKEGRYTVLAENK 91
Query: 61 ED 62
D
Sbjct: 92 SD 93
>3t57_A UDP-N-acetylglucosamine O-acyltransferase domain- protein;
LEFT-handed parallel beta helix, lipid A biosynthesis,
lipid synthesis; 2.10A {Arabidopsis thaliana}
Length = 305
Score = 26.3 bits (58), Expect = 7.7
Identities = 1/12 (8%), Positives = 4/12 (33%)
Query: 73 GVTVHTGTADGG 84
++H +
Sbjct: 120 FCSIHRSSKPSD 131
>3gb0_A Peptidase T; NP_980509.1, aminopeptidase PEPT, peptidase family
M20/M25/M structural genomics, joint center for
structural genomics; 2.04A {Bacillus cereus atcc 10987}
Length = 373
Score = 26.1 bits (58), Expect = 8.3
Identities = 8/32 (25%), Positives = 11/32 (34%), Gaps = 1/32 (3%)
Query: 51 GEGEVGGEGGEDFN-ENYEYELIGVTVHTGTA 81
+G+VG + G T H G A
Sbjct: 166 SDGKVGEIVVAAPTQAKVNAIIRGKTAHAGVA 197
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
0.320 0.136 0.419
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,263,120
Number of extensions: 185266
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 27
Length of query: 210
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 121
Effective length of database: 4,216,824
Effective search space: 510235704
Effective search space used: 510235704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.8 bits)