RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7178
(154 letters)
>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 = 103 bits (257), Expect = 6e-27
Identities = 37/143 (25%), Positives = 62/143 (43%), Gaps = 6/143 (4%)
Query: 14 STASAASSFPIPLPPPTSSDVCEGPENFTGELSSLFEISEDNDVSDNCAQRGVCGLRNLG 73
S P + C + +S + + + + GLRNLG
Sbjct: 13 GLVPRGSPTVTPTVNRENKPTCYPKAEISRLSASQ---IRNLNPVFGGSGPALTGLRNLG 69
Query: 74 NTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSS---LVDEFALLVRKMWSGQYS 130
NTC+M++ +Q L A L +YF +D + S+ + +EF ++++ +W+GQY
Sbjct: 70 NTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWTGQYR 129
Query: 131 IVHPSDFKQILGVHYPQFKDYRQ 153
+ P DFK +G QF Y Q
Sbjct: 130 YISPKDFKITIGKINDQFAGYSQ 152
>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 = 96.4 bits (240), Expect = 8e-25
Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 2/95 (2%)
Query: 61 CAQRGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSAC-SSLVDEFAL 119
+ +G+ GLRNLGNTCFM++ +Q L L +Y + L S ++LV+EFA
Sbjct: 4 KSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAK 63
Query: 120 LVRKMWSGQY-SIVHPSDFKQILGVHYPQFKDYRQ 153
L++ +W+ +V PS+FK + + P+F Y Q
Sbjct: 64 LIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ 98
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 93.5 bits (232), Expect = 1e-23
Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 3/94 (3%)
Query: 63 QRGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSS---LVDEFAL 119
Q G+CGL NLGNTCFM++ +Q L + L +YF E + + + + +A
Sbjct: 5 QPGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAE 64
Query: 120 LVRKMWSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
L+++MWSG+ + V P FK +G PQF Y+Q
Sbjct: 65 LIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQ 98
>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 = 83.5 bits (206), Expect = 6e-20
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 1/90 (1%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSSLVDEFALLVRKM 124
G GLRNLGNTCF++A +Q L + L ++ + + L + FA ++ +
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGAL 61
Query: 125 W-SGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
W V+P+ F+ + + P F Y Q
Sbjct: 62 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQ 91
>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 = 82.4 bits (203), Expect = 2e-19
Identities = 26/99 (26%), Positives = 39/99 (39%), Gaps = 8/99 (8%)
Query: 62 AQRGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTN-KSEEDSLKSSSACSSLVDEFALL 120
A CGL NLGNTC+M+A +Q + + L + + ++ + L
Sbjct: 10 AMELPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDL 69
Query: 121 VRKMWSGQYSIVHPSDFKQILGVHYPQFKD------YRQ 153
M SI P Q L + +PQF + Y Q
Sbjct: 70 FDSMDKTSSSIP-PIILLQFLHMAFPQFAEKGEQGQYLQ 107
>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 = 81.1 bits (199), Expect = 8e-19
Identities = 32/171 (18%), Positives = 61/171 (35%), Gaps = 21/171 (12%)
Query: 4 ENTWSQDECFSTASAASSFPIPLPPPTSSDVCEGPENFTGELSSLFEISEDNDVSDNCAQ 63
E+ D + + + T + E + + I E
Sbjct: 282 EDDMVLDPSLAEHLSHFGIDMLKMQKTDKTMTELEIDMNQRIGEWELIQESGVPLKPLFG 341
Query: 64 RGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSS-LVDEFALLVR 122
G G+RNLGN+C++++ +Q L + + +K E+ + + + + A L
Sbjct: 342 PGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGH 401
Query: 123 KMWSGQYSI--------------------VHPSDFKQILGVHYPQFKDYRQ 153
+ SG+YS + P FK ++G +P+F RQ
Sbjct: 402 GLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQ 452
>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 = 67.3 bits (164), Expect = 5e-14
Identities = 18/116 (15%), Positives = 38/116 (32%), Gaps = 12/116 (10%)
Query: 50 EISEDNDVSDNCAQRGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSA 109
++ V + G+ GL N+G+TCFMS+ +Q L+ + + ++ ++ K S
Sbjct: 125 DVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSP 184
Query: 110 CSSLVDEFALLVRKMWSGQYSI------------VHPSDFKQILGVHYPQFKDYRQ 153
+V +++ + Y Q
Sbjct: 185 DKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ 240
>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 = 58.4 bits (140), Expect = 5e-11
Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 5/88 (5%)
Query: 67 CGLRNLGNTCFMSAGIQSLVAASALVEYF-----TNKSEEDSLKSSSACSSLVDEFALLV 121
G +N+GNTC+++A +Q+L + L + + + +V E
Sbjct: 25 VGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSNSGAQDEEIHKQIVIEMKRCF 84
Query: 122 RKMWSGQYSIVHPSDFKQILGVHYPQFK 149
+ + + V P L YPQF
Sbjct: 85 ENLQNKSFKSVLPVVLLNTLRKCYPQFA 112
>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 = 45.6 bits (108), Expect = 1e-06
Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSSLVDEFALLVRKM 124
G GL+N G TC+M++ +Q+L + L + E S S +L F L
Sbjct: 5 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYEL---- 60
Query: 125 WSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
Q+S K + + Q
Sbjct: 61 ---QHSDKPVGTKKLTKSFGWETLDSFMQ 86
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 45.7 bits (108), Expect = 1e-06
Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 7/89 (7%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSSLVDEFALLVRKM 124
G GL+N G TC+M++ +Q+L + L + E S S +L F L
Sbjct: 174 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYEL---- 229
Query: 125 WSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
Q+S K + + Q
Sbjct: 230 ---QHSDKPVGTKKLTKSFGWETLDSFMQ 255
>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 = 29.6 bits (66), Expect = 0.40
Identities = 28/168 (16%), Positives = 54/168 (32%), Gaps = 48/168 (28%)
Query: 11 ECFSTASAASSFPIPLPPPTS--SDVCEG-------------PENFTGELSSLFEISED- 54
+ + TA + P ++ V EG +++ EL L++
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 55 -NDVSDNCAQRGVCGLRNLGNTC-----FMSAGIQSLVAASALVEYFTNKS---EEDSLK 105
D+ A+ L L T + G+ ++E+ N S ++D L
Sbjct: 184 VGDLIKFSAET----LSELIRTTLDAEKVFTQGLN-------ILEWLENPSNTPDKDYL- 231
Query: 106 SSSACSSLVDEFALLVRKMWSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
S S L+ G + H ++LG + + Y +
Sbjct: 232 LSIPIS-----CPLI------GVIQLAHYVVTAKLLGFTPGELRSYLK 268
>2dj0_A Thioredoxin-related transmembrane protein 2; AVLA237, CGI-31
protein, TXNDC14, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 137
Score = 27.1 bits (60), Expect = 1.6
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 88 ASALVEYFTNKSEEDSLKSSSACSSLVDEFALLVRKMWSG 127
+S ++YF +K+ ++ L+ + +V+ FA WS
Sbjct: 5 SSGYIKYFNDKTIDEELERDKRVTWIVEFFAN-----WSN 39
>3rao_A Putative luciferase-like monooxygenase; unknown, structural
genomics, PSI-biology, midwest center FO structural
genomics, MCSG, enzyme; 2.30A {Bacillus cereus}
Length = 371
Score = 27.4 bits (61), Expect = 2.3
Identities = 6/38 (15%), Positives = 14/38 (36%), Gaps = 9/38 (23%)
Query: 115 DEFALLVRKMWSGQYSIVHPSDFKQILGVHYPQFKDYR 152
+EF +++ +W + +K G Y +
Sbjct: 161 EEFVTILKGLWKEE-----EFSYK---GNFY-ELHHTH 189
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting,
protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP:
a.4.5.54 a.4.5.54
Length = 566
Score = 26.6 bits (57), Expect = 4.7
Identities = 8/51 (15%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 91 LVEYFTNKSEEDSLKSSSACSSLVDEFALLVRKMWSGQYSIVHPSDFKQIL 141
+ E+ ++ ++ + ++ +LVD +A+ + M G ++ P + ++
Sbjct: 415 IYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIG-TGLISPMEMREAC 464
>3ne8_A N-acetylmuramoyl-L-alanine amidase; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 1.24A {Bartonella henselae}
Length = 234
Score = 26.0 bits (58), Expect = 4.8
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 79 SAGIQSLVAA---SALVE--YFTNKSEEDSLKSSS 108
A Q L A S L+E Y +NK +E L +
Sbjct: 173 YADFQVLKAPDVPSVLIEIGYLSNKEDEKLLNNPQ 207
>3ryc_A Tubulin alpha chain; alpha-tubulin, beta-tubulin, GTPase,
microtubule, tubulin, cell cycle; HET: GTP GDP; 2.10A
{Ovis aries} PDB: 3ryf_A* 3ryh_A* 3ryi_A* 3hke_A*
3hkc_A* 3hkd_A* 3hkb_A* 3n2g_A* 3n2k_A* 1sa0_A* 1sa1_A*
3edl_F* 1ffx_A* 1ia0_A* 2hxf_A* 2hxh_A* 2p4n_A* 1jff_A*
2wbe_A* 3dco_A* ...
Length = 451
Score = 25.9 bits (57), Expect = 7.5
Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 21 SFPIPLPPPTSSDVCEGPENFTGELSSLFEISEDNDVSDNCAQRGVCGLRNLGNTCFMSA 80
F I P P S P N + E S+ + DN A +C RNL
Sbjct: 168 EFSI-YPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICR-RNLDIERPTYT 225
Query: 81 GIQSLVA 87
+ L++
Sbjct: 226 NLNRLIS 232
>2ajr_A Sugar kinase, PFKB family; TM0828, possible 1-phosphofructokinase
(EC 2.7.1.56), struct genomics, joint center for
structural genomics, JCSG; HET: MSE; 2.46A {Thermotoga
maritima} SCOP: c.72.1.1
Length = 331
Score = 25.6 bits (57), Expect = 7.6
Identities = 4/30 (13%), Positives = 8/30 (26%)
Query: 84 SLVAASALVEYFTNKSEEDSLKSSSACSSL 113
+ VA + + K A +
Sbjct: 274 AYVAGMVYYFIKHGANFLEMAKFGFASALA 303
>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis,
clathrin adaptor, transport, coated PITS; 4.0A {Mus
musculus} SCOP: i.23.1.1
Length = 158
Score = 25.1 bits (54), Expect = 9.1
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 66 VCGLRNLGNTCFMSAGIQSLVAASALVEYFTNKSEEDSLKSSSACSSLVDEF 117
C + N I V L +YF + E D + + ++DEF
Sbjct: 68 CCAIEGQDNELITLELIHRYV--ELLDKYFGSVCELDIIFNFEKAYFILDEF 117
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
0.315 0.130 0.388
Gapped
Lambda K H
0.267 0.0657 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,210,164
Number of extensions: 106664
Number of successful extensions: 215
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 19
Length of query: 154
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 69
Effective length of database: 4,328,508
Effective search space: 298667052
Effective search space used: 298667052
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: 53 (24.3 bits)