RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6196
(146 letters)
>3mca_B Protein DOM34, elongation factor 1 alpha-like protein; protein
protein complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 390
Score = 92.9 bits (230), Expect = 2e-23
Identities = 50/100 (50%), Positives = 69/100 (69%)
Query: 36 FTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEK 95
F + GR + + VKMG+YHTLDLEL+R F L K EWD+ AL+R++ ACN +
Sbjct: 74 FDTKAAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNPSR 133
Query: 96 TADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRG 135
A++ AV++ EGLANI LIT M+++R +I+ IPRKRRG
Sbjct: 134 NAEIGAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRG 173
>2vgn_A DOM34; translation termination factor, protein biosynthesis,
translation regulation, cell division, mRNA degradation;
2.5A {Saccharomyces cerevisiae} SCOP: b.38.4.1 c.55.4.2
d.79.3.2 PDB: 2vgm_A 3izq_0 3j16_A*
Length = 386
Score = 84.4 bits (208), Expect = 2e-20
Identities = 32/105 (30%), Positives = 59/105 (56%), Gaps = 5/105 (4%)
Query: 36 FTPAVGYYYYCGRNIQE-----NQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVA 90
F Y Y G + + N + +G Y + L+ F + K ++ + + A
Sbjct: 74 FDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEA 133
Query: 91 CNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRG 135
CNIE +D AAV++QEG+A++ L+T+S ++++ KIE ++P+K+R
Sbjct: 134 CNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRT 178
Score = 35.1 bits (80), Expect = 0.005
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 1 MGAYHTLDLELNRKFELSKPEWDSLYTARI 30
+G Y + L+ F + K ++ +
Sbjct: 101 VGKYLSFTLDYVYPFTIIKQNFNKFMQKLL 130
>3j15_A Protein pelota; ribosome recycling, ribosome, archaea,
translation-transport complex; HET: ADP; 6.60A
{Pyrococcus furiosus}
Length = 357
Score = 75.6 bits (185), Expect = 3e-17
Identities = 25/102 (24%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 36 FTPAVGYYYYCGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIE 94
F G + + V +G YHT+ +E + KP W +ER++ A
Sbjct: 72 FHKFANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKEAVAAS 131
Query: 95 KTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGY 136
K A V V++ +G A++ L+ + I N+ KR
Sbjct: 132 KRARVMIVVIDDGEADMALVREYGVEILNSIRHNLGGKRYNT 173
>3oby_A Protein pelota homolog; SM fold, hydrolase; 2.90A {Archaeoglobus
fulgidus}
Length = 352
Score = 70.1 bits (171), Expect = 3e-15
Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 11/101 (10%)
Query: 36 FTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEK 95
F G+ + + YHTL++ + ++ + K +W LER+ A
Sbjct: 72 FHRFANRLRVSGKIVAGI---EESGYHTLNITVGKELSIIK-KWKPEQLERLRRAVEDSN 127
Query: 96 TADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGY 136
++ + ++EG A ++R I +R GY
Sbjct: 128 RPEIVMLTIEEGYAVA-------GVLRQWGVEEIFEERMGY 161
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 70.2 bits (171), Expect = 3e-15
Identities = 18/101 (17%), Positives = 37/101 (36%), Gaps = 3/101 (2%)
Query: 36 FTPAVGYYYYCGRNIQEN-QYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIE 94
F G ++ GA+HT++L++ + + K +W+ L+R++ N
Sbjct: 86 FQEFTNRLRIHGIIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANKR 145
Query: 95 KTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRG 135
+A V E L I + ++ + G
Sbjct: 146 SRIIIALVDFDEYLIAIPFEQGIK--ILSEKSLRPLNEEEG 184
Score = 33.2 bits (75), Expect = 0.024
Identities = 8/30 (26%), Positives = 18/30 (60%)
Query: 1 MGAYHTLDLELNRKFELSKPEWDSLYTARI 30
GA+HT++L++ + + K +W+ R+
Sbjct: 109 KGAHHTINLDIGDEIIIIKQQWNKYVLDRL 138
>2qi2_A Pelota, cell division protein pelota related protein; DOM34, cell
cycle; 2.90A {Thermoplasma acidophilum} SCOP: b.38.4.1
c.55.4.2 d.79.3.2
Length = 347
Score = 67.9 bits (165), Expect = 2e-14
Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 2/101 (1%)
Query: 36 FTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEK 95
F G I+ + K G + ++ + ++ + ++K EWD ++ ++ A + +
Sbjct: 72 FQDFDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITK-EWDDQHIDLLKEATDEKY 129
Query: 96 TADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGY 136
AV M E A I LI + + K
Sbjct: 130 VTVYTAVAMDEDEAQIFLIHPYGIQQVGTVYSGRSGKYAEG 170
>3agj_B Protein pelota homolog; GTP binding, translation-hydrolase complex;
HET: GTP; 2.30A {Aeropyrum pernix}
Length = 358
Score = 62.5 bits (151), Expect = 2e-12
Identities = 14/102 (13%), Positives = 34/102 (33%), Gaps = 5/102 (4%)
Query: 36 FTPAVGYYYYCGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPE-WDSIALERIEVACNI 93
F P G G ++ +++ G H+ + + + + + W LER+
Sbjct: 69 FQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQELERLA--AGR 126
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRG 135
+ V A + + + ++ + +P K
Sbjct: 127 ARGTAVIAAVDYDE-FALAVLAGHGMKILEDTSARLPGKDDP 167
Score = 29.3 bits (65), Expect = 0.47
Identities = 4/31 (12%), Positives = 11/31 (35%), Gaps = 1/31 (3%)
Query: 1 MGAYHTLDLELNRKFELSKPE-WDSLYTARI 30
G H+ + + + + + W R+
Sbjct: 92 KGRRHSTAVSIGTWLVVERDKGWSEQELERL 122
>3agk_A Peptide chain release factor subunit 1; translation; 2.10A
{Aeropyrum pernix}
Length = 373
Score = 56.2 bits (134), Expect = 3e-10
Identities = 10/93 (10%), Positives = 29/93 (31%), Gaps = 1/93 (1%)
Query: 47 GRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQE 106
G + + + G + + D + + + ++++
Sbjct: 92 GLVLFCGEDMSTGKFECFMFSPPEPIRVFYYRTDKRFITDFLEDMVEDNN-AIGIIIVER 150
Query: 107 GLANIMLITASMSLVRTKIETNIPRKRRGYFCA 139
A I L+ + V ++E +P K + +
Sbjct: 151 DQATIGLLKGARLEVLKELEGFVPGKHKMGGQS 183
Score = 28.4 bits (62), Expect = 0.83
Identities = 2/26 (7%), Positives = 5/26 (19%)
Query: 1 MGAYHTLDLELNRKFELSKPEWDSLY 26
G + + D +
Sbjct: 103 TGKFECFMFSPPEPIRVFYYRTDKRF 128
>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 = 44.7 bits (105), Expect = 3e-06
Identities = 33/198 (16%), Positives = 60/198 (30%), Gaps = 83/198 (41%)
Query: 1 MGAYHTLDLELNRKFELSKPEWD------------SLYTARIGLKSPFTPAVGYYYYCGR 48
MG ++L + + ++ W+ S+ I + +P + + G+
Sbjct: 1631 MG------MDLYKTSKAAQDVWNRADNHFKDTYGFSI--LDIVINNPVNLTIHFGGEKGK 1682
Query: 49 NIQENQYVKMGAYHT----------LDLELNRK-----FE-----LSKPEWDSIALERIE 88
I+EN Y M + T + E+N F LS ++ AL +E
Sbjct: 1683 RIREN-YSAM-IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 89 VACNIEKTADVAAVMMQEGL---------------------ANIMLITASMSLVRTKIET 127
A + +GL A++M I + + +V
Sbjct: 1741 KAA--------FEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVF----- 1787
Query: 128 NIPRKRRGYFCATLYIVP 145
RG VP
Sbjct: 1788 -----YRGMTMQVA--VP 1798
Score = 29.6 bits (66), Expect = 0.44
Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 51 QENQYVKMGAYHTLDLELNRKFELSKPEWD 80
Q +Q MG ++L + + ++ W+
Sbjct: 1624 QGSQEQGMG------MDLYKTSKAAQDVWN 1647
Score = 28.9 bits (64), Expect = 0.71
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 49 NIQENQYV---KMGAYHTLDLELN----RKFELSK-PEWDSIALERIE 88
N++ QYV + A T+ LN +K ++ + + S++LE +E
Sbjct: 1847 NVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQK--SLSLEEVE 1892
Score = 28.1 bits (62), Expect = 1.4
Identities = 26/143 (18%), Positives = 46/143 (32%), Gaps = 33/143 (23%)
Query: 5 HTLDLELNRKFELSKPEWDSL----YTARIGLKSPFTPAVGYYYYCGRNIQENQ---YVK 57
H L +L ++ + + + L TARI K PF + R + E
Sbjct: 102 HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF--RAVGEGNAQLVAI 159
Query: 58 MG------AYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANI 111
G Y + EL ++ + E + +T A + +GL NI
Sbjct: 160 FGGQGNTDDY--FE-ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL-NI 215
Query: 112 M--------------LITASMSL 120
+ L++ +S
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISC 238
>3no0_A DNA gyrase subunit A; DNA topology, topoisomerase, C-terminal DO
gyrase, DNA binding protein, isomerase; HET: DNA GOL;
1.30A {Aquifex aeolicus}
Length = 276
Score = 28.3 bits (64), Expect = 0.82
Identities = 5/42 (11%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKI-ETNIPRKRR 134
+ ++ + +++ T + KI + +IP +
Sbjct: 211 GTKDTLVDLIPIKEEVELLITTKNGKAFYDKINQKDIPLSTK 252
>3uc1_A DNA gyrase subunit A; DNA binding protein, topoisomerase,
isomerase; HET: DNA; 1.65A {Mycobacterium tuberculosis}
Length = 327
Score = 28.3 bits (64), Expect = 0.92
Identities = 3/33 (9%), Positives = 14/33 (42%)
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
+ + ++ + + + +T+ ++RT
Sbjct: 246 RRRGRLVGALIVDDDSELYAVTSGGGVIRTAAR 278
>1zi0_A DNA gyrase subunit A; beta pinwheel, topoisomerase, spiralling beta
pinwheel, DNA wrapping, isomerase, DNA bindng protein;
HET: DNA; 2.60A {Escherichia coli}
Length = 307
Score = 28.2 bits (64), Expect = 1.0
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
E+ V + + IM+IT + +LVRT++
Sbjct: 244 ERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVS 276
>2wqd_A Phosphoenolpyruvate-protein phosphotransferase; kinase, cytoplasm,
transport, magnesium, PEP- utilising enzyme,
phosphotransferase system; 2.40A {Staphylococcus aureus}
PDB: 2hro_A
Length = 572
Score = 26.7 bits (60), Expect = 3.3
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 86 RIEVACNIEKTADVAAVM 103
E+A NI D+ V+
Sbjct: 270 HAELAANIGTPNDLPGVI 287
>2hwg_A Phosphoenolpyruvate-protein phosphotransferase; enzyme I,
phosphoenolpyruvate:sugar phosphotransferase system,
PTS; HET: NEP; 2.70A {Escherichia coli} PDB: 2kx9_A
2xdf_A 2l5h_A
Length = 575
Score = 26.7 bits (60), Expect = 3.6
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 86 RIEVACNIEKTADVAAVM 103
++EV NI DV
Sbjct: 268 QVEVCANIGTVRDVEGAE 285
>3l6v_A GYRA, DNA gyrase subunit A; gyrase A C-terminal domain, GYRA
C-terminal domain, DNA wrapping, beta-strand-bearing
proline, ATP-binding; HET: DNA; 2.19A {Xanthomonas
campestris PV}
Length = 370
Score = 26.4 bits (59), Expect = 3.6
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
E+ + ++ +MLI+ +LVRT+
Sbjct: 283 ERNGKLVRAVLLGSTDEVMLISDGGTLVRTRGS 315
>2xz9_A Phosphoenolpyruvate-protein kinase (PTS system EI component in
bacteria); thermophilic, PEP-utilising enzyme,
transferase; 1.68A {Thermoanaerobacter tengcongensis}
PDB: 2bg5_A 2xz7_A*
Length = 324
Score = 26.3 bits (59), Expect = 4.3
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 86 RIEVACNIEKTADVAAVM 103
++ +A NI DVA+ +
Sbjct: 19 KVMLAANIGTPKDVASAL 36
>3qek_A NMDA glutamate receptor subunit; amino terminal domain, ION
channel, NMDA receptor, allosteri modulation,
phenylethanolamine, polyamine; HET: NAG BMA; 2.00A
{Xenopus laevis} PDB: 3qel_A* 3qem_A* 3q41_A*
Length = 384
Score = 26.2 bits (57), Expect = 4.6
Identities = 7/31 (22%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 49 NIQENQYVKMGAYHTLDLELNRKFELSKPEW 79
N+Q + V++G ++ + N K W
Sbjct: 355 NLQNRKLVQVGIFNGSYIIQN----DRKIIW 381
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.4 bits (57), Expect = 5.2
Identities = 15/122 (12%), Positives = 37/122 (30%), Gaps = 39/122 (31%)
Query: 3 AYHTLDLELNRKFELSKPEWDSLYT------ARIGLKSPFTPAVGYYYYCGRNIQENQYV 56
+H ++E + L + ++ +I R+
Sbjct: 478 GHHLKNIEHPERMTLFR----MVFLDFRFLEQKI-----------------RHDSTAWNA 516
Query: 57 KMGAYHTL-DLELNRKF-ELSKPEWDSIA------LERIEVACNIEKTADVAAVMMQEGL 108
+TL L+ + + + P+++ + L +IE K D+ ++ L
Sbjct: 517 SGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL----LRIAL 572
Query: 109 AN 110
Sbjct: 573 MA 574
>2bco_A Succinylglutamate desuccinylase; NESG, VPR14, structural genomics,
PSI, protein structure initiative; 2.33A {Vibrio
parahaemolyticus} SCOP: c.56.5.7 PDB: 2g9d_A
Length = 350
Score = 25.3 bits (55), Expect = 8.1
Identities = 19/87 (21%), Positives = 29/87 (33%), Gaps = 7/87 (8%)
Query: 24 SLYTARIGLKSPFTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIA 83
S Y+A T +G I EN + DL L ++PE S
Sbjct: 204 SWYSAENYSAQALTMELG----RVARIGENA---LDRLTAFDLALRNLIAEAQPEHLSKP 256
Query: 84 LERIEVACNIEKTADVAAVMMQEGLAN 110
+ V+ I + D M + + N
Sbjct: 257 CIKYRVSRTIVRLHDDFDFMFDDNVEN 283
>1suu_A DNA gyrase subunit A; topoisomerase,DNA gyrase, beta-propeller,
beta-pinwheel, ISO; HET: DNA; 1.75A {Borrelia
burgdorferi} SCOP: b.68.10.1
Length = 312
Score = 25.1 bits (56), Expect = 8.6
Identities = 6/33 (18%), Positives = 12/33 (36%)
Query: 94 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
+K V + I+L++ +RT
Sbjct: 250 KKAGSVVDAIAVSEDDEILLVSKRSKALRTVAG 282
>2nvn_A Hypothetical protein; structural genomics, PSI- protein structure
initiative, joint center for structural G JCSG; 2.50A
{Synechococcus elongatus} SCOP: d.18.1.3
Length = 122
Score = 24.9 bits (54), Expect = 9.3
Identities = 3/12 (25%), Positives = 4/12 (33%)
Query: 15 FELSKPEWDSLY 26
EL+ E
Sbjct: 34 VELTAAEMADFC 45
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
0.321 0.136 0.406
Gapped
Lambda K H
0.267 0.0822 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,213,173
Number of extensions: 117031
Number of successful extensions: 249
Number of sequences better than 10.0: 1
Number of HSP's gapped: 247
Number of HSP's successfully gapped: 34
Length of query: 146
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 61
Effective length of database: 4,328,508
Effective search space: 264038988
Effective search space used: 264038988
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 (21.9 bits)
S2: 53 (24.0 bits)