RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13474
(105 letters)
>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 = 39.1 bits (90), Expect = 6e-05
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 1 MQELFSQLQSSHESALPPDALRRALAEAF--FDQQRFQLGFMD--DAAECFENMLLRIHY 56
M+ F LQ+ ++ P L L + + F ++ Q GF DA E F + +
Sbjct: 80 MKRCFENLQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLFHSMSI 139
Query: 57 HIASEEAEDMCG 68
+ +ED
Sbjct: 140 VFGDKFSEDFRI 151
>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 = 38.9 bits (90), Expect = 9e-05
Identities = 20/111 (18%), Positives = 40/111 (36%), Gaps = 16/111 (14%)
Query: 1 MQELFSQLQSSHESALPPDALRRALAEAF--FDQQRFQLGFM-DDAAECFENMLLRIHYH 57
+++LF + + S +PP L + L AF F ++ Q ++ DA EC+ M+ +
Sbjct: 66 LRDLFDSMDKTSSS-IPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQK 124
Query: 58 I------------ASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96
+ +S + K + + F + C
Sbjct: 125 LEAIEDDSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEV 175
>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 = 37.7 bits (87), Expect = 3e-04
Identities = 19/121 (15%), Positives = 34/121 (28%), Gaps = 53/121 (43%)
Query: 17 PPDAL-------RRALAEAFFDQ------QR---FQLGF-----------MDDAAECFEN 49
PP +L R+A A + DQ +R F F + A++
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINK 441
Query: 50 ML-----------LRIH-YHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSEP 97
L ++I Y + + D+ I +V+ P
Sbjct: 442 DLVKNNVSFNAKDIQIPVYD--TFDGSDLRVLSGSISER-----IVDC-------IIRLP 487
Query: 98 L 98
+
Sbjct: 488 V 488
Score = 35.0 bits (80), Expect = 0.002
Identities = 21/121 (17%), Positives = 29/121 (23%), Gaps = 40/121 (33%)
Query: 6 SQLQSSHESALPPDALRRALAEAFFDQQ----RFQLGFMDDAAE---------------- 45
SQLQ LP A + +F LG++ E
Sbjct: 31 SQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF-LGYVSSLVEPSKVGQFDQVLNLCLT 89
Query: 46 CFENMLLR---IHYHIASEEAEDMCGAKHCIPHEKFAMTLVEQSVC----GACGATSEPL 98
FEN L IH A + E + + + A P
Sbjct: 90 EFENCYLEGNDIHALAAK------------LLQENDTTLVKTKELIKNYITARIMAKRPF 137
Query: 99 P 99
Sbjct: 138 D 138
Score = 30.0 bits (67), Expect = 0.13
Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 26/97 (26%)
Query: 3 ELFSQLQ--SSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENML--LRIHYHI 58
EL S L+ + H L A+ A+AE D F ++ + + + I
Sbjct: 262 ELRSYLKGATGHSQGLVT-AV--AIAET------------DSWESFFVSVRKAITVLFFI 306
Query: 59 ASEEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATS 95
P+ +++E S+ G S
Sbjct: 307 GVR-------CYEAYPNTSLPPSILEDSLENNEGVPS 336
>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 = 36.4 bits (84), Expect = 6e-04
Identities = 14/96 (14%), Positives = 26/96 (27%), Gaps = 13/96 (13%)
Query: 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIAS 60
+Q +F +LQ S + + F + D E +L + +
Sbjct: 53 LQRVFYELQHSDKPVGTKKLTKS------FGWETLDSFMQHDVQELCRVLLDNVENKMKG 106
Query: 61 EEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96
E + F +V C S+
Sbjct: 107 TCVE-------GTIPKLFRGKMVSYIQCKEVDYRSD 135
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 33.4 bits (76), Expect = 0.007
Identities = 14/96 (14%), Positives = 26/96 (27%), Gaps = 13/96 (13%)
Query: 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIAS 60
+Q +F +LQ S + + F + D E +L + +
Sbjct: 222 LQRVFYELQHSDKPVGTKKLTKS------FGWETLDSFMQHDVQELCRVLLDNVENKMKG 275
Query: 61 EEAEDMCGAKHCIPHEKFAMTLVEQSVCGACGATSE 96
E + F +V C S+
Sbjct: 276 TCVE-------GTIPKLFRGKMVSYIQCKEVDYRSD 304
>2eui_A Probable acetyltransferase; dimer, structural genomics, PSI,
protein structure initiative; 2.80A {Pseudomonas
aeruginosa PAO1} SCOP: d.108.1.1
Length = 153
Score = 26.2 bits (58), Expect = 1.7
Identities = 6/43 (13%), Positives = 17/43 (39%)
Query: 3 ELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAE 45
LF + + + P++ R+ L + ++ + D +
Sbjct: 16 PLFVKYREFYGMLSYPESSRKFLEKRLRRKESVIYLALADEED 58
>3mm5_B Sulfite reductase, dissimilatory-type subunit BET;
alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A
{Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B*
3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*
Length = 366
Score = 26.1 bits (58), Expect = 2.4
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 40 MDDAAECFENMLLRIHYHIASEEAEDMCGAKHC 72
MD+ E F + L I+ +MCGA H
Sbjct: 155 MDELYEYFTDHKLPAMCRISLACCANMCGAVHA 187
>2y9k_A Protein INVG; protein transport, type III secretion system, outer
membrane secretin family, C15 fold; 8.30A {Salmonella
enterica subsp}
Length = 137
Score = 25.2 bits (55), Expect = 3.3
Identities = 2/30 (6%), Positives = 8/30 (26%)
Query: 14 SALPPDALRRALAEAFFDQQRFQLGFMDDA 43
+ + L + + + L +
Sbjct: 82 RNVSLNEFNNFLKRSGLYNKNYPLRGDNRK 111
>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate
reduction, oxidored sulfite reduction; HET: SRM; 1.76A
{Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B*
Length = 386
Score = 25.4 bits (56), Expect = 3.9
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 40 MDDAAECFENMLLRIHYHIASEEAEDMCGAKHC 72
MD+ E F +M L ++ +MCGA HC
Sbjct: 166 MDELFEEFTSMRLPAIVRVSLACCINMCGAVHC 198
>2hy5_B Intracellular sulfur oxidation protein DSRF; DSRE, DSRF, sulfur,
structural genomics, PSI, protein initiative, berkeley
structural genomics center, BSGC, TRAN; 1.72A
{Allochromatium vinosum} SCOP: c.114.1.1 PDB: 2hyb_B
Length = 136
Score = 25.0 bits (54), Expect = 4.7
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 4 LFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDA 43
++ ++ + + +AL L A FDQ + F+DD
Sbjct: 9 MYLNRKAPYGTIYAWEALEVVLIGAAFDQD-VCVLFLDDG 47
>2d1p_B TUSC, hypothetical UPF0116 protein YHEM; tRNA modification,
sulfur transfer, structural genomics, translation;
2.15A {Escherichia coli} SCOP: c.114.1.1
Length = 119
Score = 24.4 bits (53), Expect = 6.6
Identities = 8/40 (20%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 4 LFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDA 43
F + H +A + L LA + + F+ D
Sbjct: 5 AFVFSTAPHGTAAGREGLDALLATSALTDD-LAVFFIADG 43
>3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Ruegeria pomeroyi}
Length = 681
Score = 25.0 bits (55), Expect = 6.7
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 82 LVEQSVCGACGATSEPLPFTQE 103
LVEQ + A G EPL TQ
Sbjct: 308 LVEQMIRVAAG---EPLSITQG 326
>3ls9_A Triazine hydrolase; atrazine chlorohydrolase TRZN; 1.40A
{Arthrobacter aurescens} PDB: 3lsc_A* 3lsb_A*
Length = 456
Score = 24.5 bits (54), Expect = 8.6
Identities = 4/20 (20%), Positives = 7/20 (35%)
Query: 52 LRIHYHIASEEAEDMCGAKH 71
+R+H H M +
Sbjct: 233 VRLHTHFYEPLDAGMSDHLY 252
>3mg1_A OCP, orange carotenoid protein; carotenoid binding protein,
echinone, phycobilisome; HET: ECH; 1.65A {Synechocystis
SP} PDB: 3mg2_A* 3mg3_A* 1m98_A*
Length = 323
Score = 24.3 bits (52), Expect = 9.3
Identities = 11/42 (26%), Positives = 13/42 (30%), Gaps = 5/42 (11%)
Query: 17 PPDALRRALAEAFFDQ-----QRFQLGFMDDAAECFENMLLR 53
P A LAE + Q M D A + L R
Sbjct: 55 APGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCR 96
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
0.322 0.133 0.403
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,627,719
Number of extensions: 88541
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 35
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
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 (22.0 bits)
S2: 51 (23.5 bits)