RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5641
(192 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 = 144 bits (365), Expect = 5e-42
Identities = 59/152 (38%), Positives = 88/152 (57%), Gaps = 10/152 (6%)
Query: 36 VSLSSNDIRVLPPKPLLFANGDKVPGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQ 95
LS++ IR L P G P + GLRN GNTC++N+ILQCL + LA+YF +
Sbjct: 41 SRLSASQIRNLNPV-----FGGSGPALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNC 95
Query: 96 YKIDMSRRNKFNSKKYGTKGEVTEQLAVLLKSIWSCSYNPDISNQFKVIIDKYGTQYRGN 155
Y+ D++R N G KGEV E+ +++K++W+ Y FK+ I K Q+ G
Sbjct: 96 YQDDINRSNLL-----GHKGEVAEEFGIIMKALWTGQYRYISPKDFKITIGKINDQFAGY 150
Query: 156 NQHDAQEFLMWLLDKVHEDLNTATKKKYKTIK 187
+Q D+QE L++L+D +HEDLN A +K +
Sbjct: 151 SQQDSQELLLFLMDGLHEDLNKADNRKRYKEE 182
>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 = 133 bits (336), Expect = 3e-38
Identities = 50/134 (37%), Positives = 76/134 (56%), Gaps = 8/134 (5%)
Query: 55 NGDKVPGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTK 114
N G+ GLRN GNTCF+N+ILQCLS+T L +Y + Y D+ +
Sbjct: 2 NSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS-------NAH 54
Query: 115 GEVTEQLAVLLKSIWSCSYNPDIS-NQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHE 173
+ E+ A L+++IW+ S N +S ++FK I +Y ++ G NQ DAQEFL +LLD +H
Sbjct: 55 TALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHN 114
Query: 174 DLNTATKKKYKTIK 187
++N T + +
Sbjct: 115 EVNRVTLRPKSNPE 128
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 133 bits (335), Expect = 7e-38
Identities = 55/128 (42%), Positives = 77/128 (60%), Gaps = 5/128 (3%)
Query: 60 PGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTE 119
PG+ GL N GNTCF+N+ LQCLS+T L +YF+ D+Y+ +++R N G KGE+ E
Sbjct: 6 PGLCGLGNLGNTCFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPL-----GMKGEIAE 60
Query: 120 QLAVLLKSIWSCSYNPDISNQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHEDLNTAT 179
A L+K +WS FK + ++ Q+ G Q D+QE L +LLD +HEDLN
Sbjct: 61 AYAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVK 120
Query: 180 KKKYKTIK 187
KK Y +K
Sbjct: 121 KKPYLELK 128
>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 = 115 bits (290), Expect = 2e-31
Identities = 39/133 (29%), Positives = 70/133 (52%), Gaps = 9/133 (6%)
Query: 61 GVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTEQ 120
G +GLRN GNTCF+NA+LQCLS T L ++ + ++ ++ G E+TE
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEV--------PGGGRAQELTEA 53
Query: 121 LAVLLKSIWSCSYNPDIS-NQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHEDLNTAT 179
A ++ ++W ++ +F+ + KY + G +Q DAQEFL L++++H ++N
Sbjct: 54 FADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRG 113
Query: 180 KKKYKTIKVKTPK 192
++ +
Sbjct: 114 RRAPPILANGPVP 126
>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 = 115 bits (289), Expect = 2e-30
Identities = 33/143 (23%), Positives = 57/143 (39%), Gaps = 27/143 (18%)
Query: 60 PGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTE 119
PG G+RN GN+C++N+++Q L +V KI F + + +
Sbjct: 342 PGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKI-------FQNAPTDPTQDFST 394
Query: 120 QLAVLLKSIWSCSYNPDISN--------------------QFKVIIDKYGTQYRGNNQHD 159
Q+A L + S Y+ + FK +I K ++ N Q D
Sbjct: 395 QVAKLGHGLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQD 454
Query: 160 AQEFLMWLLDKVHEDLNTATKKK 182
AQEF + L++ V + ++
Sbjct: 455 AQEFFLHLINMVERNCRSSENPN 477
>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 = 105 bits (262), Expect = 3e-27
Identities = 26/129 (20%), Positives = 44/129 (34%), Gaps = 18/129 (13%)
Query: 64 GLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTEQLAV 123
GL N GNTC++NA +QC+ L + +Y + + + +T L
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDAL--KRYAGALRASGEM-----ASAQYITAALRD 68
Query: 124 LLKSIWSC--SYNPDISNQFKVIIDKYGTQYRGNN------QHDAQEFLMWLLDKVHEDL 175
L S+ S P + Q+ Q DA E + ++ + + L
Sbjct: 69 LFDSMDKTSSSIPP---IILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKL 125
Query: 176 NTATKKKYK 184
K
Sbjct: 126 EAIEDDSVK 134
>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 = 101 bits (254), Expect = 8e-26
Identities = 32/182 (17%), Positives = 60/182 (32%), Gaps = 10/182 (5%)
Query: 15 SNNMCSTYDHSMSCRRQAYGLVSLSSNDIRVLPPKPLLFANGDKVPGVIGLRNHGNTCFI 74
C Y ++ A + + P + ++ G+ GL N G+TCF+
Sbjct: 100 FCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVP------SMERRDGLSGLINMGSTCFM 153
Query: 75 NAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTEQLAVLLKSIWSCSYN 134
++ILQCL H + + + + R+ V E L S S
Sbjct: 154 SSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSST 213
Query: 135 ----PDISNQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHEDLNTATKKKYKTIKVKT 190
K G +Q DA EF ++++++H+ + +
Sbjct: 214 STNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANN 273
Query: 191 PK 192
+
Sbjct: 274 KQ 275
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 71.5 bits (175), Expect = 5e-15
Identities = 28/126 (22%), Positives = 44/126 (34%), Gaps = 15/126 (11%)
Query: 58 KVPGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEV 117
K G +GL+N G TC++N++LQ L T+ L + + + D S ++ V
Sbjct: 171 KHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKS------------V 218
Query: 118 TEQLAVLLKSIWSCSYNPDISNQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHEDLNT 177
L + + K QHD QE LLD V +
Sbjct: 219 PLALQRVFYELQHSDKPVGTKKLTKSFG---WETLDSFMQHDVQELCRVLLDNVENKMKG 275
Query: 178 ATKKKY 183
+
Sbjct: 276 TCVEGT 281
>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 = 69.1 bits (169), Expect = 2e-14
Identities = 28/126 (22%), Positives = 45/126 (35%), Gaps = 15/126 (11%)
Query: 58 KVPGVIGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEV 117
K G +GL+N G TC++N++LQ L T+ L + + + D S ++ V
Sbjct: 2 KHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKS------------V 49
Query: 118 TEQLAVLLKSIWSCSYNPDISNQFKVIIDKYGTQYRGNNQHDAQEFLMWLLDKVHEDLNT 177
L + + K + QHD QE LLD V +
Sbjct: 50 PLALQRVFYELQHSDKPVGTKKLTKSFGWE---TLDSFMQHDVQELCRVLLDNVENKMKG 106
Query: 178 ATKKKY 183
+
Sbjct: 107 TCVEGT 112
>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 = 67.6 bits (164), Expect = 8e-14
Identities = 21/129 (16%), Positives = 49/129 (37%), Gaps = 10/129 (7%)
Query: 63 IGLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTEQLA 122
+G +N GNTC++NA LQ L + L + + +S + + + + ++
Sbjct: 25 VGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSNSGAQDEEIHKQ---IVIEMK 81
Query: 123 VLLKSIWSCSYNPDISNQFKVIIDKYGTQYRGNN-------QHDAQEFLMWLLDKVHEDL 175
+++ + S+ + + K Q+ + Q DA+E L +
Sbjct: 82 RCFENLQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLFHSMSIVF 141
Query: 176 NTATKKKYK 184
+ ++
Sbjct: 142 GDKFSEDFR 150
>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 = 33.1 bits (75), Expect = 0.055
Identities = 25/121 (20%), Positives = 35/121 (28%), Gaps = 50/121 (41%)
Query: 28 CRRQ-AYGLVSLSSNDIRVLPPKPLL--FANGDKVP----GVIGLRNHGNTCFI---NAI 77
R AY SL PP L N + VP + L ++ N+
Sbjct: 308 VRCYEAYPNTSL--------PPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSH 359
Query: 78 LQCLSHTDI-L---AEYFVL-----------------------DQYKIDMSRR-----NK 105
L +I L A+ V+ DQ +I S R N+
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR 419
Query: 106 F 106
F
Sbjct: 420 F 420
Score = 30.0 bits (67), Expect = 0.55
Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 31/81 (38%)
Query: 119 EQLAVLLKSI-----WSCS---YNPDISNQFKVIIDKYGTQY--RGNNQHDAQEFLMWLL 168
E L +++ + W YN + NQ QY G+ + A L
Sbjct: 1824 EALQYVVERVGKRTGWLVEIVNYN--VENQ----------QYVAAGDLR--A-------L 1862
Query: 169 DKVHEDLNTATKKKYKTIKVK 189
D V LN +K I+++
Sbjct: 1863 DTVTNVLNFIKLQKIDIIELQ 1883
>2vhf_A Ubiquitin carboxyl-terminal hydrolase CYLD; cytokine signalling,
linkage specificity, deubiquitinating enzyme, Lys63-
linked, anti-oncogene; 2.8A {Homo sapiens}
Length = 374
Score = 29.7 bits (66), Expect = 0.49
Identities = 22/118 (18%), Positives = 41/118 (34%), Gaps = 27/118 (22%)
Query: 64 GLRNHGNTCFINAILQCLSHTDILAEYFVLDQYKIDMSRRNKFNSKKYGTKGEVTEQLAV 123
G++ H N+C++++ L CL F + R K + +E +
Sbjct: 11 GIQGHYNSCYLDSTLFCL---------FAFSSVLDTVLLRPKEKN----DVEYYSETQEL 57
Query: 124 LLKSIWSCSYNP---------DISNQFKVIIDKYG-TQYRGNNQHDAQEFLMWLLDKV 171
L I NP + + I++K + + D +EFL L +
Sbjct: 58 LRTEI----VNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHHI 111
>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast
structural genomics consortiu PSI-2, protein structure
initiative, hydrolase; NMR {Mus musculus}
Length = 86
Score = 26.3 bits (58), Expect = 2.3
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 29 RRQAYGLVSLSSNDIRVL---PPKPLLFANGDKVPGVIGLRN 67
+ Q + ++ R+L PP+ L ++ D G + +++
Sbjct: 27 QGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQS 68
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 27.7 bits (61), Expect = 3.2
Identities = 8/34 (23%), Positives = 10/34 (29%)
Query: 113 TKGEVTEQLAVLLKSIWSCSYNPDISNQFKVIID 146
TK EV + N DI +I
Sbjct: 187 TKKEVKAAATAAMTKATETVDNKDIERFIPSLIQ 220
>2xu0_A Erythrocyte membrane protein 1; adhesion, virulence,
duffy-binding-like-DO; 2.06A {Plasmodium falciparum palo
alto}
Length = 487
Score = 27.0 bits (60), Expect = 4.5
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 152 YRGNNQHDAQEFLMWLLDKVHEDLNTATKKKYK 184
+ N Q+ L + K+++ L +K Y
Sbjct: 209 FLPNKDDKVQKGLQVVFKKIYKSLTPEARKHYA 241
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
0.319 0.134 0.400
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,819,545
Number of extensions: 155838
Number of successful extensions: 421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 21
Length of query: 192
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 104
Effective length of database: 4,244,745
Effective search space: 441453480
Effective search space used: 441453480
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 (21.7 bits)
S2: 54 (25.0 bits)