RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17307
(342 letters)
>3mca_B Protein DOM34, elongation factor 1 alpha-like protein; protein
protein complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 390
Score = 213 bits (542), Expect = 3e-66
Identities = 128/311 (41%), Positives = 178/311 (57%), Gaps = 50/311 (16%)
Query: 82 LRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQ 141
+ +E EDMWH YN++ GD ++AST+R+V TGS++ SRV L I VE++DFDT+
Sbjct: 18 MCPEEPEDMWHLYNILQVGDQLKASTVRRVVKVGATGSTSGSRVVMKLRILVENMDFDTK 77
Query: 142 ACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADV 201
A L +KGR + + VKMG+YHTLDLEL+R F L K EWD+ AL+R++ ACN + A++
Sbjct: 78 AAQLHIKGRTTEYHPEVKMGSYHTLDLELHRNFTLYKNEWDAFALDRVDAACNPSRNAEI 137
Query: 202 AAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKD--------------------- 240
AV++ EGLANI LIT M+++R +I+ IPRKRR +
Sbjct: 138 GAVVLDEGLANICLITDYMTILRQRIDQVIPRKRRGDSSAYQKGLDKFYDSVFQSINSEF 197
Query: 241 --------------LLKELLSPITTVEAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEIL 286
+ L AVK+D K ++++K+KF+++HSS+ HSL EIL
Sbjct: 198 DFDKLKVVILASPGFVARGLYDYIFSMAVKLDLKQIVKSKNKFVILHSSTGHIHSLNEIL 257
Query: 287 ADPTVTSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIADCL 331
DP V SK+ DTK D +A+YG HV A E AI LLI+D L
Sbjct: 258 KDPAVESKLADTKYVQEIRVLNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSL 317
Query: 332 FRNSDLNERKK 342
FR+SD+ RKK
Sbjct: 318 FRSSDIATRKK 328
>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 = 206 bits (524), Expect = 1e-63
Identities = 77/317 (24%), Positives = 140/317 (44%), Gaps = 58/317 (18%)
Query: 82 LRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQ 141
L ++ ED++ Y ++ + D + + + S L I V S DFD +
Sbjct: 20 LLPEDKEDLFTVYQIVDKDDELIFKKKFTSKLDE--AGKKKSTDLVKLKIKVISEDFDMK 77
Query: 142 ACVLRLKGRNIQE-----NQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIE 196
L+ KG + + N + +G Y + L+ F + K ++ + + ACNIE
Sbjct: 78 DEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIE 137
Query: 197 KTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDN---------KDLLKELLS 247
+D AAV++QEG+A++ L+T+S ++++ KIE ++P+K+R + K + S
Sbjct: 138 YKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYS 197
Query: 248 PITTV---------------------------EAVKMDNKVLLENKSKFLLVHSSSAFKH 280
+ A + NK +L+NK F + H S+ +
Sbjct: 198 AMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQ 257
Query: 281 SLKEILADPTVTSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTL 325
+ E+L +P SK+QDTK D +A+YG + V A E AI L
Sbjct: 258 GINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYL 317
Query: 326 LIADCLFRNSDLNERKK 342
L+ D + + ++ +R++
Sbjct: 318 LLTDKVLHSDNIAQREE 334
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 173 bits (439), Expect = 2e-51
Identities = 61/306 (19%), Positives = 113/306 (36%), Gaps = 40/306 (13%)
Query: 70 VESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTML 129
+ D QA L ++ +D+W + ++ + D V A T R V S R+ +
Sbjct: 23 ILEFDEKRQAVKLHIESEDDLWLLHLILEKDDKVVAKTTRDVG-----LGKESRRIPMTI 77
Query: 130 TISVESIDFDTQACVLRLKGRNIQEN-QYVKMGAYHTLDLELNRKFELSKPEWDSIALER 188
+ V+ +F LR+ G ++ GA+HT++L++ + + K +W+ L+R
Sbjct: 78 ILKVDYTEFQEFTNRLRIHGIIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDR 137
Query: 189 IEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLSP 248
++ N +A V E L I + ++ K + + + E+ +
Sbjct: 138 LKRQANKRSRIIIALVDFDEYLIAIPFEQ-GIKILSEKSLRPLNEEEGIIEQNALEIATE 196
Query: 249 IT----------TVEAVKMDNKVLLEN-------KSKFLLVHSSSAFKHSLKEILADPTV 291
+ + A K + K + SSA + L E+L +
Sbjct: 197 LAEYVKQYDPDAILLAGPGFFKEEVSKKVNAILKNKKIYIDSVSSATRAGLHEVLKRDII 256
Query: 292 TSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSD 336
M D + A P YG V A E A++T+L+ + L + D
Sbjct: 257 DKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLLSS-D 315
Query: 337 LNERKK 342
ER
Sbjct: 316 EQERLT 321
>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 = 171 bits (434), Expect = 1e-50
Identities = 53/305 (17%), Positives = 108/305 (35%), Gaps = 37/305 (12%)
Query: 70 VESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESN-TGSSTSSRVRTM 128
+ D +R++ +D+W+ N+++EGD V A T R+V+ ++ S R+
Sbjct: 3 ILEEDLKNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPIT 62
Query: 129 LTISVESIDFDTQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALER 188
+ + VE I+F LR+ G I+ + K G + ++ + ++ + ++K EWD ++
Sbjct: 63 IRLKVEKIEFQDFDNRLRILGTVIEGPEDTK-GKHQSITVTVDSEISITK-EWDDQHIDL 120
Query: 189 IEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLSP 248
++ A + + AV M E A I LI + + K +
Sbjct: 121 LKEATDEKYVTVYTAVAMDEDEAQIFLIHPYGIQQVGTVYSGRSGKYAEGNYSEASYFDQ 180
Query: 249 ITTV------------------EAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILADPT 290
I + + + F + S ++ E +
Sbjct: 181 IVNALKNYSNSIIILGPGFARDRFARYCAQRGVNVIGSFPANRTDS---GAVYEFITSAD 237
Query: 291 VTSKMQDTKA-------------LDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSDL 337
+ + + + YG +A + A+ L+I D +FR D
Sbjct: 238 GAKLLSNERIARDKEIVDEFLVAVKKDMGVYGRDQTESALQMGALSDLIITDEMFRTEDG 297
Query: 338 NERKK 342
Sbjct: 298 RRSLS 302
Score = 96.0 bits (238), Expect = 1e-22
Identities = 22/86 (25%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESN-TGSSTS 59
M+++ +++ K+ + E +D+W+ N+++EGD V A T R+V+ ++ S
Sbjct: 1 MRILEEDL----KNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRER 56
Query: 60 SRVRTMLTISVESIDFDTQACVLRLK 85
R+ + + VE I+F LR+
Sbjct: 57 ERIPITIRLKVEKIEFQDFDNRLRIL 82
>3oby_A Protein pelota homolog; SM fold, hydrolase; 2.90A {Archaeoglobus
fulgidus}
Length = 352
Score = 171 bits (433), Expect = 1e-50
Identities = 61/292 (20%), Positives = 106/292 (36%), Gaps = 49/292 (16%)
Query: 82 LRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQ 141
L + +D+WH +I +GD V A+T R QS S V L I VE ++F
Sbjct: 17 LIPETLDDLWHLRFIIEKGDVVFATTKRASQSSD-KLRSDKEMVTVRLGIEVEKVEFHRF 75
Query: 142 ACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADV 201
A LR+ G+ + + YHTL++ + ++ + K +W LER+ A ++
Sbjct: 76 ANRLRVSGKIVAGI---EESGYHTLNITVGKELSIIK-KWKPEQLERLRRAVEDSNRPEI 131
Query: 202 AAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRD--------NKDLLKELLSPITTV- 252
+ ++EG A ++R I +R K+ E+ + + +
Sbjct: 132 VMLTIEEGYAVA-------GVLRQWGVEEIFEERMGYGKGMGDSRKEFFGEVAAKLESFD 184
Query: 253 --------------EAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILADPTVTSKMQDT 298
+ + + E ++V SS EIL V + +
Sbjct: 185 FKYLIVAGPGFAKNDFLDFLKERYPEMAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEV 244
Query: 299 KAL--------------DPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSD 336
+ R YG V A+ +AI+ LL+AD
Sbjct: 245 RLAEEAEYIDRLLEGIAKGERVAYGLDEVREAHNYRAIEVLLVADEFLLEER 296
>3agj_B Protein pelota homolog; GTP binding, translation-hydrolase complex;
HET: GTP; 2.30A {Aeropyrum pernix}
Length = 358
Score = 170 bits (432), Expect = 2e-50
Identities = 58/312 (18%), Positives = 104/312 (33%), Gaps = 46/312 (14%)
Query: 70 VESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTML 129
VE +D + LR + ED+W + GD VR T R V GS RV L
Sbjct: 5 VEVLDNKRRIVRLRPESEEDLWLLRITLRPGDVVRKRTSRDVP----VGSGRKERVVMTL 60
Query: 130 TISVESIDFDTQACVLRLKGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPE-WDSIALE 187
I ++SI+F LR+ G ++ +++ G H+ + + + + + W LE
Sbjct: 61 RIRLDSIEFQPFTGKLRISGIVVEGPDEFGVKGRRHSTAVSIGTWLVVERDKGWSEQELE 120
Query: 188 RIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLS 247
R+ + V A + + + ++ + +P K +++ E
Sbjct: 121 RLA--AGRARGTAVIAAVDYDE-FALAVLAGHGMKILEDTSARLPGKDDPSREQEVEKYV 177
Query: 248 PITTVEAVKMDNKVLLE----------------------NKSKFLLVHSSSAFKHSLKEI 285
V+ + K V +S ++E
Sbjct: 178 DRAAKRIVEEAARHRSPIAVIAGPGQLKTSVAEKVQRAMPSLKVATVDTSMGGVAGVREA 237
Query: 286 LADPTVTSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIADC 330
L +VT +++ A Y V A A+DT+L+ D
Sbjct: 238 LRRESVTRILRELSIVEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDT 297
Query: 331 LFRNSDLNERKK 342
L + D R+
Sbjct: 298 LLHSPDDAVREA 309
>3j15_A Protein pelota; ribosome recycling, ribosome, archaea,
translation-transport complex; HET: ADP; 6.60A
{Pyrococcus furiosus}
Length = 357
Score = 169 bits (428), Expect = 7e-50
Identities = 65/297 (21%), Positives = 116/297 (39%), Gaps = 42/297 (14%)
Query: 82 LRLKESEDMWHAYNLITEGDSVRASTIRKV-QSESNTGSSTSSRVRTMLTISVESIDFDT 140
++ + +D+WH Y++I GD V A T+RK Q + + + L + E I+F
Sbjct: 15 VKAETLDDLWHLYHIIDPGDIVYAKTLRKQAQRADSLRAEKVEVIPVFLGVQAEKINFHK 74
Query: 141 QACVLRLKGRNIQ-ENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTA 199
A +R+ G + + V +G YHT+ +E + KP W +ER++ A K A
Sbjct: 75 FANQVRVTGPIVYASREDVPLGKYHTIAIEQGTVVTIQKPRWKEHHIERLKEAVAASKRA 134
Query: 200 DVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDN----------KDLLKELL--- 246
V V++ +G A++ L+ + I N+ KR + D+ K +
Sbjct: 135 RVMIVVIDDGEADMALVREYGVEILNSIRHNLGGKRYNTDRESEEMKFFHDVAKTMEEVM 194
Query: 247 -----------SPITTVEAV-KMDNKVLLENKSKFLLVHSSSAFKHSLKEILADPTVTSK 294
P E K + E K ++ +S + + E++ V
Sbjct: 195 KRENVEKAIVAGPGFVKEDFYKFLKEKYPELAKKVVIEDTSVTGRTGIYEVIKRGVVDRV 254
Query: 295 MQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSD 336
Q+ + A + YG + V A A++TLL+ D L +
Sbjct: 255 YQENRVAKEVQLVEKVLENIARNNGLVAYGLKEVEEAVNYGAVETLLVLDELLKGEL 311
>3agk_A Peptide chain release factor subunit 1; translation; 2.10A
{Aeropyrum pernix}
Length = 373
Score = 72.4 bits (176), Expect = 2e-14
Identities = 41/328 (12%), Positives = 81/328 (24%), Gaps = 72/328 (21%)
Query: 86 ESEDMWHAYNLITEGDSVRAS-------------TIRKVQSESNTGSSTSSRVRTMLTIS 132
+ L+ E A + V + S + ++ T
Sbjct: 10 LTISKRELARLLKELKKWSAPATVLLSLYIPPGRPLSDVMTLLRQEYSITDNIKLKRTRQ 69
Query: 133 VESIDFDTQACVLRL------KGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIAL 186
L++ G + + + G + + D +
Sbjct: 70 AVKRALSAAMDRLQMLTSTPPNGLVLFCGEDMSTGKFECFMFSPPEPIRVFYYRTDKRFI 129
Query: 187 ERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNK------- 239
+ + ++++ A I L+ + V ++E +P K +
Sbjct: 130 TDFLEDMVEDNN-AIGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYE 188
Query: 240 ---------------DLLKELLSPITTVEAVK-----------------MDNKVLLENKS 267
+ LL P+ +K L+
Sbjct: 189 RIIEQMVDEFFKKVGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLDYRLKKIL 248
Query: 268 KFLLVHSSSAFKHSLKEILADPT-------------VTSKMQDTKALDPSRAFYGYRHVS 314
LV + LKE + + + A YG + V
Sbjct: 249 APELVDVAYQGLQGLKEAVMKAEKVVEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVE 308
Query: 315 AANESQAIDTLLIADCLFRNSDLNERKK 342
AA E A+ TLLI + + E+ K
Sbjct: 309 AALEMGAVKTLLIHESREDLEEWVEKAK 336
>1x52_A Pelota homolog, CGI-17; ERF1_3 domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.79.3.2
Length = 124
Score = 55.9 bits (135), Expect = 4e-10
Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 15/74 (20%)
Query: 284 EILADPTVTSKMQDTK---------------ALDPSRAFYGYRHVSAANESQAIDTLLIA 328
+ TV S++ DTK +P RAFYG + V ANE+ AIDTLLI+
Sbjct: 2 SSGSSGTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLLIS 61
Query: 329 DCLFRNSDLNERKK 342
D LFR+ D+ R +
Sbjct: 62 DELFRHQDVATRSR 75
>3e20_C Eukaryotic peptide chain release factor subunit 1; SUP35, SUP45,
translation termination, peptide release, GTP-
nucleotide-binding; 3.50A {Schizosaccharomyces pombe}
Length = 441
Score = 50.4 bits (119), Expect = 4e-07
Identities = 38/324 (11%), Positives = 85/324 (26%), Gaps = 79/324 (24%)
Query: 86 ESEDMWHAYNLITEGDSVRAS-----------------TIRKVQSESNTGSSTSSRV-RT 127
++ ++W L+ + + + + E T S+ SRV R
Sbjct: 15 KAIEIWKIRRLVKQLINCHGNGTSMITLIIPPGEQISRYSNMLAEEYGTASNIKSRVNRL 74
Query: 128 MLTISVESI-------DFDTQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPE 180
+ ++ S + ++ G I E + +D E + S+
Sbjct: 75 SVLSAITSTRERLKLYNKVPDNGLVIYCGEVIMEGNKTRK---LNIDFEPFKPINTSQYL 131
Query: 181 WDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDN-- 238
D+ +A +E ++M +++ S V + ++P+K
Sbjct: 132 CDN-KFHTEALAELLESDQRFGFIVMDGHQTLYGVVSGSAREVLQRFTVDLPKKHGRGGQ 190
Query: 239 ----------------------------------KDLLKELLSPITTVEAVKMDNKVLLE 264
L + +
Sbjct: 191 SALRFARLRDEKRHNYVRKVAEGAVQHFITDDKPNVAGIVLAGSADFKTELGQSDLFDQR 250
Query: 265 NKSKFL-LVHSSSAFKHSLKEILADPT-------------VTSKMQDTKALDPSRAFYGY 310
+S+ + V S + + + + D +LD + +G
Sbjct: 251 LQSRIIKTVDVSYGGDAGFNQAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYCFGV 310
Query: 311 RHVSAANESQAIDTLLIADCLFRN 334
A + A++TLL L
Sbjct: 311 VDTMNALQEGAVETLLCFADLDMI 334
>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 = 49.1 bits (116), Expect = 1e-06
Identities = 55/422 (13%), Positives = 124/422 (29%), Gaps = 107/422 (25%)
Query: 10 DKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKV-------QSESN------TGS 56
+ S + + E+ + +++ + A+ + R K+ + N GS
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS 161
Query: 57 STSSRVRTMLTISVESIDFDTQAC---------VLRLKESED----MWHAYNLITEGDSV 103
+ + + V + Q + E + I +
Sbjct: 162 GKTW-----VALDVCL-SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215
Query: 104 RASTIRKVQSESNTGSSTSSRV------RTMLTI-----SVESID-FDTQAC-VLRLKGR 150
R+ ++ ++ + R+ L + + ++ + F+ C +L L R
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS-CKIL-LTTR 273
Query: 151 NIQENQYVKMGAYHTLDLELNRKFELSKPE-------WDSIALERI-EVACNIEKTA-DV 201
Q ++ + L+ + L+ E + + + +
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSM-TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI 332
Query: 202 AAVMMQEGLA--------NIMLITASMSLVRTKIETNIPRKR-------RDNKDLLKELL 246
A +++GLA N +T + +E RK + + LL
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392
Query: 247 S------PITTVEAV--KMDNKVLLENKSKFLLVHSSSAFKHSLKEILADPTVTSKM--- 295
S + V V K+ L+E + K + S + ++ + + +
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH 452
Query: 296 -QDTKALDPSRA--------FY---GYRHVSAANESQAIDTLLIADCLFRNSDLN----E 339
K D FY G+ H+ + + LFR L+ E
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGH-HLKNIEHPERMT-------LFRMVFLDFRFLE 504
Query: 340 RK 341
+K
Sbjct: 505 QK 506
Score = 40.6 bits (94), Expect = 8e-04
Identities = 36/258 (13%), Positives = 74/258 (28%), Gaps = 84/258 (32%)
Query: 145 LRLKGRNIQENQYVK---MGAY--HTLDLE--LNRKFELSKPE---WDSIALERIEVACN 194
LR ++ + V + + L+ L+ K + W ++ CN
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK------NCN 193
Query: 195 IEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLSP------ 248
+ V+ L ++ R+ +NI + + L+ LL
Sbjct: 194 SPE-----TVLEM--LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 249 --I-------TTVEAVKMDNKVLL-------------ENKSKFLLVHSSSAFKHS-LKEI 285
+ A + K+LL + L H S +K +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306
Query: 286 LA-----------------DPTVTS----KMQDTKALDPSRAFYGYRHVSAANESQAIDT 324
L +P S ++D + ++HV+ + I++
Sbjct: 307 LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD----GLATWDN-WKHVNCDKLTTIIES 361
Query: 325 LLIADCLFRNSDLNERKK 342
L + L + E +K
Sbjct: 362 SL--NVL----EPAEYRK 373
Score = 35.2 bits (80), Expect = 0.030
Identities = 46/337 (13%), Positives = 99/337 (29%), Gaps = 107/337 (31%)
Query: 1 MKLVHKNINDKDKSGVVALVPEESEDMWH--AYNLIAEGDSVRASTI---RKVQSESNTG 55
L+ K ++ + + +P E + ++IAE +T + V +
Sbjct: 304 KSLLLKYLDCRPQD-----LPREVLTT-NPRRLSIIAESIRDGLATWDNWKHVNCD---- 353
Query: 56 SSTSSRVRTMLTISVESIDF-DTQACVLRL---KESED--------MWHAYNLITEGDSV 103
++ T++ S+ ++ + + RL S +W +++I V
Sbjct: 354 -----KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW--FDVIKSDVMV 406
Query: 104 RASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNIQE------NQY 157
+ + K S + TIS+ SI + L++K N + Y
Sbjct: 407 VVNKLHK--------YSLVEKQPKESTISIPSIYLE-----LKVKLENEYALHRSIVDHY 453
Query: 158 VKMG--------------------AYHTLDLELNRKFELSKP-----EWDSIALERIEVA 192
+H ++E + L + + + A
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA 513
Query: 193 CNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNKDLLKELLSPITTV 252
N + + + Q + + I N P+ R +L L
Sbjct: 514 WN--ASGSILNTLQQ------------LKFYKPYICDNDPKYERLVNAILDFLPKI---- 555
Query: 253 EAVKMDNKVLLENKSKFL-LVHSSSAFKHSLKEILAD 288
+ L+ SK+ L+ A + I +
Sbjct: 556 ------EENLI--CSKYTDLLR--IALMAEDEAIFEE 582
>3ir9_A Peptide chain release factor subunit 1; structural genomics,
APC36528.1, C-terminal domain, PSI-2, protein structure
initiative; 2.21A {Methanosarcina mazei}
Length = 166
Score = 33.9 bits (77), Expect = 0.036
Identities = 10/42 (23%), Positives = 16/42 (38%)
Query: 293 SKMQDTKALDPSRAFYGYRHVSAANESQAIDTLLIADCLFRN 334
D + YG V A E ++D LL+++ L
Sbjct: 34 RDFFKELIADSGKVAYGESQVRANLEINSVDVLLLSEDLRAE 75
>3qby_A Hepatoma-derived growth factor-related protein 2; HDGF2, structural
genomics consortium, SGC, protein binding; HET: M3L;
1.95A {Homo sapiens} PDB: 3qj6_A* 3eae_A 1n27_A
Length = 94
Score = 28.1 bits (62), Expect = 1.2
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 260 KVLLENKSKFLLVHSSSAFKHSLKEILADPTV 291
+ K K+ + F L EI +P
Sbjct: 60 FPYDKCKDKYGKPNKRKGFNEGLWEIQNNPHA 91
>1ri0_A Hepatoma-derived growth factor; HDGF, HATH domain, PWWP domain,
heparin-binding, hormone/growth factor complex; NMR
{Homo sapiens} SCOP: b.34.9.2 PDB: 2b8a_A 2nlu_A
Length = 110
Score = 28.2 bits (62), Expect = 1.6
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 262 LLENKSKFLLVHSSSAFKHSLKEILADPTV 291
E+K KF + F L EI +PTV
Sbjct: 76 YEESKEKFGKPNKRKGFSEGLWEIENNPTV 105
>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 = 28.4 bits (63), Expect = 3.6
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 138 FDTQACVLRL-KGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIE 196
+ QA + L + I EN + DL L ++PE S + V+ I
Sbjct: 211 YSAQALTMELGRVARIGENA---LDRLTAFDLALRNLIAEAQPEHLSKPCIKYRVSRTIV 267
Query: 197 KTADVAAVMMQEGLAN 212
+ D M + + N
Sbjct: 268 RLHDDFDFMFDDNVEN 283
>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 = 27.5 bits (62), Expect = 6.5
Identities = 5/43 (11%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 196 EKTADVAAVMMQEGLANIMLITASMSLVRTKI-ETNIPRKRRD 237
+ ++ + +++ T + KI + +IP +
Sbjct: 211 GTKDTLVDLIPIKEEVELLITTKNGKAFYDKINQKDIPLSTKK 253
>3uc1_A DNA gyrase subunit A; DNA binding protein, topoisomerase,
isomerase; HET: DNA; 1.65A {Mycobacterium tuberculosis}
Length = 327
Score = 27.5 bits (62), Expect = 6.6
Identities = 3/33 (9%), Positives = 14/33 (42%)
Query: 196 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 228
+ + ++ + + + +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 = 27.4 bits (62), Expect = 6.6
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 196 EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 228
E+ V + + IM+IT + +LVRT++
Sbjct: 244 ERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVS 276
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
0.314 0.126 0.341
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: 4,666,775
Number of extensions: 259123
Number of successful extensions: 601
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 39
Length of query: 342
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 248
Effective length of database: 4,077,219
Effective search space: 1011150312
Effective search space used: 1011150312
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (25.9 bits)