RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 013441
(443 letters)
>2o5r_A Glutamyl-tRNA synthetase 1; TM1351, EC 6.1.1.17, glutamate-T ligase
1, glurs 1, structural genomics, joint center for ST
genomics, JCSG; 2.34A {Thermotoga maritima}
Length = 481
Score = 627 bits (1619), Expect = 0.0
Identities = 181/386 (46%), Positives = 258/386 (66%), Gaps = 7/386 (1%)
Query: 41 VAASLSTNTNKVDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLE 100
+ + + + VRVRFAPSPTG LHVGGARTALFN+LFAR + GKF+LRIEDTDLE
Sbjct: 2 GSDKIHHHHHH---MVRVRFAPSPTGFLHVGGARTALFNFLFARKEKGKFILRIEDTDLE 58
Query: 101 RSTKESEEAVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCF 160
RS +E EE +++ L WLGL WDEGP VGGD+GPYRQSER +Y+++A++L++ G Y +
Sbjct: 59 RSEREYEEKLMESLRWLGLLWDEGPDVGGDHGPYRQSERVEIYREHAERLVKEGKAYYVY 118
Query: 161 CSNEELEKMKEIAKLKQLPPVYTGKWA--TATDAEVQKELERGTPYTYRFRVPKGGSLKI 218
EE+E+M+E + P Y+ + T ++ E+G F++P+ + +
Sbjct: 119 AYPEEIEEMREKLLSEGKAPHYSQEMFEKFDTPERRREYEEKGLRPAVFFKMPRKDYV-L 177
Query: 219 SDLIRGEVSWNLDTLGDFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQAL 278
+D+++GEV + +GDFVIMRSNG P YNF VDD M I+HVIR ++HL NTLRQ
Sbjct: 178 NDVVKGEVVFKTGAIGDFVIMRSNGLPTYNFACVVDDMLMEITHVIRGDDHLSNTLRQLA 237
Query: 279 IYKALGFSMPYFAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDG 338
+Y+A + P FAHVS IL PD KLSKRHGATSV FR+MGYLP+A+VNYLALLGW
Sbjct: 238 LYEAFEKAPPVFAHVSTILGPDGKKLSKRHGATSVEAFRDMGYLPEALVNYLALLGWSHP 297
Query: 339 TENEFFTLKQLVEKFTIERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWKSTG 398
E TL++L+ F+++R++ + AIFD KL+WMNG +LR +P +L +L ++ G
Sbjct: 298 EGKELLTLEELISSFSLDRLSPNPAIFDPQKLKWMNGYYLRNMPIEKLAELAKPFFEKAG 357
Query: 399 ILTESKGPFVDEAIQLLKDGIDLVPD 424
I + + +++ K+ ++++ +
Sbjct: 358 IKIID-EEYFKKVLEITKERVEVLSE 382
>2ja2_A Glutamyl-tRNA synthetase; non-discriminating glutamyl-tRNA
aminoacylation, protein biosynthesis, aminoacyl-tRNA
synthetase, ligase; 1.65A {Mycobacterium tuberculosis}
PDB: 3pny_A 3pnv_A
Length = 498
Score = 622 bits (1606), Expect = 0.0
Identities = 146/375 (38%), Positives = 210/375 (56%), Gaps = 7/375 (1%)
Query: 55 QVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDL 114
VRVRF PSPTG HVG RTALFN+ +AR GG FV RIEDTD +R ++ES A+L L
Sbjct: 6 TVRVRFCPSPTGTPHVGLVRTALFNWAYARHTGGTFVFRIEDTDAQRDSEESYLALLDAL 65
Query: 115 SWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAK 174
WLGLDWDEGP VGG YGPYRQS+R +Y+ +LL +G Y F + EE+E A
Sbjct: 66 RWLGLDWDEGPEVGGPYGPYRQSQRAEIYRDVLARLLAAGEAYHAFSTPEEVEARHV-AA 124
Query: 175 LKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLG 234
+ Y TDA+ L G R R+P L +DL+RG V++ ++
Sbjct: 125 GRNPKLGYDNFDRHLTDAQRAAYLAEGRQPVVRLRMPD-DDLAWNDLVRGPVTFAAGSVP 183
Query: 235 DFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKAL-----GFSMPY 289
DF + R++G P+Y DDA M I+HV+R E+ LP+T RQ +++AL +P
Sbjct: 184 DFALTRASGDPLYTLVNPCDDALMKITHVLRGEDLLPSTPRQLALHQALIRIGVAERIPK 243
Query: 290 FAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQL 349
FAH+ +L KLSKR +++ R+ G++P+ ++NYLALLGW +++ F L ++
Sbjct: 244 FAHLPTVLGEGTKKLSKRDPQSNLFAHRDRGFIPEGLLNYLALLGWSIADDHDLFGLDEM 303
Query: 350 VEKFTIERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWKSTGILTESKGPFVD 409
V F + VN S A FD K +N +H+R + + T + + + G
Sbjct: 304 VAAFDVADVNSSPARFDQKKADALNAEHIRMLDVGDFTVRLRDHLDTHGHHIALDEAAFA 363
Query: 410 EAIQLLKDGIDLVPD 424
A +L++ I ++ D
Sbjct: 364 AAAELVQTRIVVLGD 378
>1j09_A Glutamyl-tRNA synthetase; glurs-ATP-Glu complex, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, ligase; HET: GLU ATP; 1.80A {Thermus
thermophilus} SCOP: a.97.1.1 c.26.1.1 PDB: 1n75_A*
1n77_A* 1n78_A* 2cuz_A* 2cv0_A* 2cv1_A* 2cv2_A* 2dxi_A*
1g59_A 1gln_A
Length = 468
Score = 612 bits (1581), Expect = 0.0
Identities = 148/370 (40%), Positives = 228/370 (61%), Gaps = 8/370 (2%)
Query: 56 VRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDLS 115
V R APSPTG+ HVG A ALFNY +AR GG+F++RIEDTD R +EE +L L
Sbjct: 2 VVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALK 61
Query: 116 WLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAKL 175
WLGL +DEGP VGG +GPYRQSER LY++YA++LL+ G YR F + EELE++++
Sbjct: 62 WLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEK-- 119
Query: 176 KQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLGD 235
Y G+ E ++ RG P+ R +VP+ G+ ++ D +RG V ++ + D
Sbjct: 120 ----GGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPD 175
Query: 236 FVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPYFAHVSL 295
V+++S+G P Y+ VDD M ++ VIRAEE L +T L+Y+A G+ P F H+ L
Sbjct: 176 VVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPL 235
Query: 296 ILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQLVEKFTI 355
+ PD++K+SKR TS+ ++ G+LP+A+ NYL L+G+ E FTL++ ++ FT
Sbjct: 236 LRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTW 295
Query: 356 ERVNKSGAIFDSTKLRWMNGQHLR-AIPSNELTKLIGERWKSTGILTESKGPFVDEAIQL 414
ERV+ G +FD KLRWMNG+++R + E+ + + + G+ + ++ A++L
Sbjct: 296 ERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGL-SWESEAYLRRAVEL 354
Query: 415 LKDGIDLVPD 424
++ D + +
Sbjct: 355 MRPRFDTLKE 364
>4g6z_A Glutamate-tRNA ligase; aminoacyl-tRNA synthetase, AARS, class 1B
AARS, ATP-dependen charging, protein synthesis,
structural genomics; HET: GLU; 2.05A {Burkholderia
thailandensis}
Length = 490
Score = 604 bits (1561), Expect = 0.0
Identities = 155/406 (38%), Positives = 226/406 (55%), Gaps = 12/406 (2%)
Query: 36 RRRFSVAASLSTNTNKVDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIE 95
+ + + VR RFAPSPTG +H+G R+AL+ + FAR G FVLRIE
Sbjct: 6 HHHMGTLEAQTQGPGSMTRPVRTRFAPSPTGFIHLGNIRSALYPWAFARKMKGTFVLRIE 65
Query: 96 DTDLERSTKESEEAVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGH 155
DTD+ERS++E+ +A+L+ ++WLGLD+DEGP Y Q +R Y++ ++ E G
Sbjct: 66 DTDVERSSQEAVDAILEGMAWLGLDYDEGP--------YYQMQRMDRYREVLAQMQEKGL 117
Query: 156 VYRCFCSNEELEKMKEIAKLKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGS 215
VY C+ S EEL+ ++E + P Y G W +V E G RFR P G+
Sbjct: 118 VYPCYMSTEELDALRERQRAAGEKPRYDGTWRPEPG-KVLPEPPAGVAPVLRFRNPLTGT 176
Query: 216 LKISDLIRGEVSWNLDTLGDFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLR 275
+ D ++G V + + L D V+ R +G P+YNFCV VDD M I+HVIR ++H+ NT R
Sbjct: 177 VAWDDAVKGRVEISNEELDDLVVARPDGTPMYNFCVVVDDLDMGITHVIRGDDHVNNTPR 236
Query: 276 QALIYKALGFSMPYFAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGW 335
Q I +ALG +P +AH+ +L K+SKRHGA SV +R+ GYLP+A++NYLA LGW
Sbjct: 237 QINILRALGGEVPVYAHLPTVLNEQGEKMSKRHGAMSVMGYRDAGYLPEAVLNYLARLGW 296
Query: 336 GDGTENEFFTLKQLVEKFTIERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWK 395
G + E FT +Q VE F +E + KS A +D KL W+N +++ L L +
Sbjct: 297 SHG-DAEIFTREQFVEWFDLEHLGKSPAQYDHNKLNWLNNHYIKEADDARLAGLAKPFFA 355
Query: 396 STGI--LTESKGPFVDEAIQLLKDGIDLVPDSDKALSNLLSYPLRD 439
+ GI +GP + + L+KD V + + + P
Sbjct: 356 ALGIDAGAIEQGPDLVSVMGLMKDRASTVKEIAENSAMFYRAPAPG 401
>2cfo_A Glutamyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase,
ATP-binding, nucleotide-B; HET: GLU; 2.45A
{Synechococcus elongatus}
Length = 492
Score = 598 bits (1545), Expect = 0.0
Identities = 168/379 (44%), Positives = 221/379 (58%), Gaps = 19/379 (5%)
Query: 56 VRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDLS 115
VRVR APSPTGNLH+G ARTA+FN+L+AR +GGKF+LRIEDTD ERS E E +L+ L
Sbjct: 2 VRVRLAPSPTGNLHIGTARTAVFNWLYARHRGGKFILRIEDTDRERSRPEYTENILEGLQ 61
Query: 116 WLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAKL 175
WLGL WDEGP Y QS+R LY+Q LL+ G Y C+C+ EELE ++ K
Sbjct: 62 WLGLTWDEGP--------YFQSDRLDLYRQAIQTLLDKGLAYYCYCTPEELEALRAEQKA 113
Query: 176 KQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTL-G 234
K P Y + T E G RF++ ++ DL+RG VSW L G
Sbjct: 114 KGQAPRYDNRHRHLTPEEQAAFEAAGRTPVIRFKIEDDRQIEWQDLVRGRVSWQGADLGG 173
Query: 235 DFVIMRSN-----GQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPY 289
D VI R+ G P+YN V VDD M I+ VIR E+H+ NT +Q L+Y+ALG + P
Sbjct: 174 DMVIARAAPRGEIGYPLYNLVVVVDDIAMGITDVIRGEDHIGNTPKQILLYEALGATPPN 233
Query: 290 FAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGW--GDGTENEFFTLK 347
FAH LIL KLSKR G TS+ FR MGYL A+ NY+ LLGW +G E FTL
Sbjct: 234 FAHTPLILNSTGQKLSKRDGVTSISDFRAMGYLAPALANYMTLLGWSPPEGVG-ELFTLD 292
Query: 348 QLVEKFTIERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWKSTGIL--TESKG 405
+ F+ ER+NK+GA FD KL W+N Q+++ + E + W+ G E
Sbjct: 293 LAAKHFSFERINKAGARFDWDKLNWLNRQYIQQLEPEEFLAELIPLWQGAGYAFDEERDR 352
Query: 406 PFVDEAIQLLKDGIDLVPD 424
P++ + QLL+ G++ + +
Sbjct: 353 PWLFDLAQLLQPGLNTLRE 371
>3al0_C Glutamyl-tRNA(Gln) amidotransferase subunit C, GL tRNA synthetase
2; protein-RNA complex, ligase-RNA complex; HET: GSU;
3.37A {Thermotoga maritima}
Length = 592
Score = 589 bits (1522), Expect = 0.0
Identities = 168/371 (45%), Positives = 231/371 (62%), Gaps = 20/371 (5%)
Query: 55 QVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDL 114
VRVRFAPSPTG+LHVGGARTALFN++FAR +GGKF+LRIEDTD ERS++E E+ +L+ L
Sbjct: 129 LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESL 188
Query: 115 SWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAK 174
W GLDWDEGP +GGD+GPYRQSER +Y++YA+KL+E Y E+ K
Sbjct: 189 RWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKEDPSKELFTTY 248
Query: 175 LKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLG 234
+ E+G P T +F+V G DL++G + ++ TL
Sbjct: 249 -----------------EYPHEYKEKGHPVTIKFKVLP-GKTSFEDLLKGYMEFDNSTLE 290
Query: 235 DFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPYFAHVS 294
DF+IM+SNG P YNF V VDD M ISHV R E+HL NT +Q +IY+A G+ P F H+
Sbjct: 291 DFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIP 350
Query: 295 LILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQLVEKFT 354
LIL DR+ LSKRHGATSV FR G L +A++NYLALLGW + E FT+++ ++ F
Sbjct: 351 LILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGD-EIFTIEEKLQSFD 409
Query: 355 IERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWKSTGI-LTESKGPFVDEAIQ 413
+ ++ G IFD KL W+NG+H+R I +L + E K G + + E ++
Sbjct: 410 PKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLR 469
Query: 414 LLKDGIDLVPD 424
+ ++ ++ +
Sbjct: 470 ICREKVNTLSQ 480
>3afh_A Glutamyl-tRNA synthetase 2; protein-substrate complex,
aminoacyl-tRNA synthetase, ATP-binding, ligase,
nucleotide-binding; HET: GSU; 2.00A {Thermotoga
maritima} PDB: 3akz_B*
Length = 488
Score = 584 bits (1509), Expect = 0.0
Identities = 168/371 (45%), Positives = 231/371 (62%), Gaps = 20/371 (5%)
Query: 55 QVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDL 114
VRVRFAPSPTG+LHVGGARTALFN++FAR +GGKF+LRIEDTD ERS++E E+ +L+ L
Sbjct: 25 LVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESL 84
Query: 115 SWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAK 174
W GLDWDEGP +GGD+GPYRQSER +Y++YA+KL+E Y E+ K
Sbjct: 85 RWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKEDPSKELFTTY 144
Query: 175 LKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLG 234
+ E+G P T +F+V G DL++G + ++ TL
Sbjct: 145 -----------------EYPHEYKEKGHPVTIKFKVLP-GKTSFEDLLKGYMEFDNSTLE 186
Query: 235 DFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPYFAHVS 294
DF+IM+SNG P YNF V VDD M ISHV R E+HL NT +Q +IY+A G+ P F H+
Sbjct: 187 DFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIP 246
Query: 295 LILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQLVEKFT 354
LIL DR+ LSKRHGATSV FR G L +A++NYLALLGW + E FT+++ ++ F
Sbjct: 247 LILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGD-EIFTIEEKLQSFD 305
Query: 355 IERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGERWKSTGI-LTESKGPFVDEAIQ 413
+ ++ G IFD KL W+NG+H+R I +L + E K G + + E ++
Sbjct: 306 PKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLR 365
Query: 414 LLKDGIDLVPD 424
+ ++ ++ +
Sbjct: 366 ICREKVNTLSQ 376
>1nzj_A Hypothetical protein YADB; Zn cluster, glutamyl T-RNA synthetase,
structural genomics, unknown function; 1.50A
{Escherichia coli} SCOP: c.26.1.1 PDB: 2zlz_A* 4a91_A*
Length = 298
Score = 418 bits (1077), Expect = e-146
Identities = 84/319 (26%), Positives = 142/319 (44%), Gaps = 35/319 (10%)
Query: 53 DGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQ 112
D Q RFAPSP+G LH G AL +YL AR++ G++++RIED D R + E +L+
Sbjct: 3 DTQYIGRFAPSPSGELHFGSLIAALGSYLQARARQGRWLVRIEDIDPPREVPGAAETILR 62
Query: 113 DLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEI 172
L GL WD QS+R+ Y++ L E G Y C C+ ++ +
Sbjct: 63 QLEHYGLHWDGDV--------LWQSQRHDAYREALAWLHEQGLSYYCTCTRARIQSIG-- 112
Query: 173 AKLKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDT 232
+Y G R R + +D +RG + +
Sbjct: 113 -------GIYDGHCRVLHHGP--------DNAAVRIRQQHP-VTQFTDQLRGIIHADEKL 156
Query: 233 -LGDFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPYFA 291
DF+I R +G YN V VDD ++ ++R + + T+RQ +Y+ G+ +P +
Sbjct: 157 AREDFIIHRRDGLFAYNLAVVVDDHFQGVTEIVRGADLIEPTVRQISLYQLFGWKVPDYI 216
Query: 292 HVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQL-- 349
H+ L L P +KLSK++ A ++ + L A+ +L + F+++Q+
Sbjct: 217 HLPLALNPQGAKLSKQNHAPALPKGDPRPVLIAAL-QFLGQQAEAHW---QDFSVEQILQ 272
Query: 350 --VEKFTIERVNKSGAIFD 366
V+ + + V +S +
Sbjct: 273 SAVKNWRLTAVPESAIVNS 291
>3aii_A Glutamyl-tRNA synthetase; amino-acyl tRNA synthetase, ligase; 1.65A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 553
Score = 138 bits (350), Expect = 5e-36
Identities = 86/288 (29%), Positives = 124/288 (43%), Gaps = 79/288 (27%)
Query: 52 VDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVL 111
V G+V +RFAP+P+G LH+G AR A+ N+ +AR G+ +LRIEDTD R E+ + +
Sbjct: 93 VKGEVVLRFAPNPSGPLHIGHARAAILNHEYARKYDGRLILRIEDTDPRRVDPEAYDMIP 152
Query: 112 QDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKE 171
DL WLG++WDE QS+R Y +Y +KL+E G Y C C EE ++K
Sbjct: 153 ADLEWLGVEWDE---------TVIQSDRMETYYEYTEKLIERGGAYVCTCRPEEFRELK- 202
Query: 172 IAKLKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVP-------------KGGS--- 215
RG R K GS
Sbjct: 203 ---------------------------NRGEACHCRSLGFRENLQRWREMFEMKEGSAVV 235
Query: 216 -LKISDLIRGEVSWNLDTLGDFVIMRSNGQ------------PVYNFCVTVDDATMAISH 262
+K DL N + D+V MR P+ NF V VDD + ++H
Sbjct: 236 RVKT-DL----NHPNP-AIRDWVSMRIVEAEHPRTGTRYRVYPMMNFSVAVDDHLLGVTH 289
Query: 263 VIRAEEHLPNTLRQALIYKALGFSMPY---FAHVSLILAPDRSKLSKR 307
V+R ++HL N +Q +Y+ LG+ P + + + D LS
Sbjct: 290 VLRGKDHLANREKQEYLYRHLGWEPPEFIHYGRLKM----DDVALSTS 333
>1qtq_A GLNRS, protein (glutaminyl-tRNA synthetase); glutamine, trnaGln, E.
coli, complex, ligase/RNA complex; HET: QSI; 2.25A
{Escherichia coli} SCOP: b.53.1.2 c.26.1.1 PDB: 1gsg_P*
1gts_A* 1gtr_A* 1zjw_A* 1o0b_A* 1o0c_A* 1qru_A* 1qrs_A*
1qrt_A* 1euy_A* 1euq_A* 1exd_A* 2rd2_A* 2re8_A* 1nyl_A
Length = 553
Score = 78.8 bits (195), Expect = 7e-16
Identities = 35/124 (28%), Positives = 56/124 (45%), Gaps = 14/124 (11%)
Query: 50 NKVDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEE- 108
+ V RF P P G LH+G A++ N+ A+ G+ LR +DT+ KE E
Sbjct: 21 SGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPV---KEDIEY 77
Query: 109 --AVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEEL 166
++ D+ WLG W DY + Q L+ YA +L+ G Y + E++
Sbjct: 78 VESIKNDVEWLGFHWSGNVRYSSDY--FDQ-----LH-AYAIELINKGLAYVDELTPEQI 129
Query: 167 EKMK 170
+ +
Sbjct: 130 REYR 133
>2hz7_A Glutaminyl-tRNA synthetase; rossmann fold, GLNRS core, class I
aminoacyl-tRNA synthetase, ligase; 2.30A {Deinococcus
radiodurans}
Length = 851
Score = 77.2 bits (190), Expect = 3e-15
Identities = 41/124 (33%), Positives = 62/124 (50%), Gaps = 14/124 (11%)
Query: 50 NKVDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLERSTKESEE- 108
+V RF P P+G H+G +L ++ AR GG+F LR++DT+ E +E
Sbjct: 61 AGKYPRVVTRFPPDPSGYAHLGHVFASLLDFNTARQYGGQFNLRMDDTNPE---LARQEY 117
Query: 109 --AVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEEL 166
++ DL WLGLDW E DY + + Y YA++L+ G Y S EEL
Sbjct: 118 VDSIADDLKWLGLDWGEHFYYASDY--FDR-----YY-AYAEQLIRQGDAYVESVSPEEL 169
Query: 167 EKMK 170
+++
Sbjct: 170 SRLR 173
>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 = 64.9 bits (157), Expect = 3e-11
Identities = 83/540 (15%), Positives = 157/540 (29%), Gaps = 172/540 (31%)
Query: 28 QSSVYYCKRRRFSVAASLSTNTNKVDGQVRVRF-APSPTGNLHVGGARTALFN--YLFAR 84
Q + +F V L N + ++ PS +++ R L+N +FA+
Sbjct: 75 QEEMVQ----KF-VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE-QRDRLYNDNQVFAK 128
Query: 85 SKGGKFVLRIED-TDLERSTKESEEAVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLY 143
V R++ L ++ E L+ + +D GV G G + +
Sbjct: 129 ----YNVSRLQPYLKLRQALLE-----LRPAKNVLID-----GVLG-SG--KTWVALDVC 171
Query: 144 KQYADKLLESGHVY-----RCFCSNEELEKMKEIAKLKQLPPVYTGKWATATDAEVQKEL 198
Y + ++ C LE ++++ L Q+ P +T + +++ +++
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL--LYQIDPNWTSRSDHSSNIKLRIHS 229
Query: 199 ERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLGDFVIMRSNGQPVYNFC---VT--- 252
+ P L + V N F N C +T
Sbjct: 230 IQAELRRLLKSKPYENCLLVLL----NV-QNAKAWNAF-----NLS-----CKILLTTRF 274
Query: 253 --VDDATMAISHVIRAEEHLPNTLRQ----ALIYKALG---FSMPYFA------HVSLIL 297
V D A + + +H TL +L+ K L +P +S+I
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
Query: 298 A-----PDRSKLSKRHG--------ATSVGQ---------FREMGYLPQ-----AMVNYL 330
K +S+ F + P ++ L
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL--L 392
Query: 331 ALLGWGDGTENE-FFTLKQLVEKFTIERVNKSGAI------------------------- 364
+L+ W D +++ + +L + +E+ K I
Sbjct: 393 SLI-WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD 451
Query: 365 -------FDSTKLR-------WMN--GQHLRAIPSNELTKLIGE-----RW-----KSTG 398
FDS L + + G HL+ I E L R+ +
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDS 511
Query: 399 ILTESKGPFVDEAIQL-----------------LKDGIDLVPDSDKALSNLLSYPLRDTL 441
+ G ++ QL + +D +P K NL+ D L
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP---KIEENLICSKYTDLL 568
Score = 38.7 bits (89), Expect = 0.004
Identities = 31/225 (13%), Positives = 58/225 (25%), Gaps = 61/225 (27%)
Query: 90 FVLRIEDTD-----LER----STKESEEAVLQDLSWLGL---DWDEGPGVGGDYGPYRQS 137
V L K V+ L L E Y +
Sbjct: 379 SVFP-PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES--TISIPSIYLEL 435
Query: 138 ERNSLYKQYA-DKLLESGHVYRCFCSNEELEKMKEIAKLKQLPPVYTGKW--------AT 188
+ + +++ ++ + F S++ +PP +
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDL------------IPPYLDQYFYSHIGHHLKN 483
Query: 189 ATDAEVQKELERGTPYT-YRFRVPKGGSLKISDLIRGEVSWNLDTLGDFVIMRSNGQPVY 247
E + +RF K ++ L+TL + Y
Sbjct: 484 IEHPERMTLFRM--VFLDFRFLEQK---IRHDSTAWNASGSILNTLQQLKFYKP-----Y 533
Query: 248 NFCVTVDDATM-----AISH-VIRAEEHL---PNT--LRQALIYK 281
+ +D AI + + EE+L T LR AL+ +
Sbjct: 534 ---ICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAE 575
>1irx_A Lysyl-tRNA synthetase; beta sandwitch, zinc-binding structure,
rossmann fold, alpha-helix CAGE; 2.60A {Pyrococcus
horikoshii} SCOP: a.97.1.2 c.26.1.1
Length = 523
Score = 57.2 bits (137), Expect = 5e-09
Identities = 35/284 (12%), Positives = 89/284 (31%), Gaps = 23/284 (8%)
Query: 63 SPTGNLHVGGAR-----TALFNYLFARSKGGKFVLRIEDTDLERSTKESEEAVLQDLSWL 117
+P+G +HVG R + + L + + + +D D R + +D +L
Sbjct: 29 TPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKD--YL 86
Query: 118 GLDWDEGPGVGGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSNEELEKMKEIAKLKQ 177
G+ E P G + Y + +++ +++ + G ++E ++ + +++
Sbjct: 87 GMPISEVPDPWGCHESYAE----HFMRKFEEEVEKLGIEVDLLYASELYKRGEYSEEIRL 142
Query: 178 LPPVYTGKWATATD--AEVQKELERGTPYTYRFRVPKGG--SLKISDLIRGEVSW--NLD 231
++ + P+ + I +V +
Sbjct: 143 AFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEG 202
Query: 232 TLGDFVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPNT----LRQALIYKALGFSM 287
G I N + + + + + ++HL + +I + G
Sbjct: 203 HEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEA 262
Query: 288 PYFAHVSLILAP-DRSKLSKRHGATSVGQFREMGYLPQAMVNYL 330
P + + K+S G + L +V ++
Sbjct: 263 PLSLMYEFVGIKGQKGKMSGSKGNVILLS-DLYEVLEPGLVRFI 305
>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 = 51.2 bits (122), Expect = 6e-07
Identities = 73/463 (15%), Positives = 132/463 (28%), Gaps = 161/463 (34%)
Query: 40 SVAASLSTNTNKVDGQVR--VRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDT 97
++AA L + + + ++ NY+ AR + + ++
Sbjct: 103 ALAAKLLQENDTTLVKTKELIK-------------------NYITARIMAKRPFDKKSNS 143
Query: 98 DLERSTKESEE---AVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQYA---DKLL 151
L R+ E A+ G G G DY E LY+ Y L+
Sbjct: 144 ALFRAVGEGNAQLVAI------FG-----GQGNTDDY----FEELRDLYQTYHVLVGDLI 188
Query: 152 ESGHVYRCFCSNEELEKMKEIAKLKQLPPVYT-----GKWATATDAEVQKELERGTPYTY 206
+ S E L ++ I V+T +W Y
Sbjct: 189 KF--------SAETLSEL--IRTTLDAEKVFTQGLNILEWLENPSN------TPDKDY-- 230
Query: 207 RFRVPKGGSLKISDLIRGEVSWNLDTLGDF----VIMRSNGQPVYNFCVTVDDATMAISH 262
L+ +S L + V + G + AT
Sbjct: 231 --------------LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 263 VIRA--------EEHLPNTLRQALIYKAL---GF-SMPYFAHVSLILAPDRSKLSKRHGA 310
++ A E ++R+A+ L G + + S L P + S +
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAI--TVLFFIGVRCYEAYPNTS--LPPSILEDSLENNE 332
Query: 311 TSVGQFREMGYLPQAMVNYLALLGWGDGTENEFFTLKQLVEKFTIERVNK----SGAIFD 366
P M L++ T +Q+ + + + + N +
Sbjct: 333 GV----------PSPM---LSISN---------LTQEQV-QDY-VNKTNSHLPAGKQVEI 368
Query: 367 STKLRWMNGQHLRAI----PSNELTKLIG--ERWKSTGILTESKGPFVDEAI-------- 412
S L NG + + P L L + K+ L +S+ PF + +
Sbjct: 369 S--LV--NGA--KNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP 422
Query: 413 -------QLLKDGIDLVPDSDKALSNL------LSYPLRDTLT 442
LL DL+ + D +N+ + P+ DT
Sbjct: 423 VASPFHSHLLVPASDLI-NKDLVKNNVSFNAKDIQIPVYDTFD 464
Score = 39.3 bits (91), Expect = 0.003
Identities = 49/264 (18%), Positives = 92/264 (34%), Gaps = 77/264 (29%)
Query: 214 GSLKISDLIRGEVSWNLDTLGD-FVIMRSNGQPVYNFCVTVDDATMAISHVIRAEEHLPN 272
GSL+ L+ + L + F + +P F DD AE
Sbjct: 14 GSLEHVLLVPTASFFIASQLQEQFN--KILPEPTEGF--AADDEPTTP-----AE----- 59
Query: 273 TLRQALIYKALGFSMPYFAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPQAMVNYLA- 331
L+ K LG+ VS ++ P + + + +F E YL ++ LA
Sbjct: 60 -----LVGKFLGY-------VSSLVEPSKVGQFDQVLNLCLTEF-ENCYLEGNDIHALAA 106
Query: 332 -LLGWGDGTENE-------FFTLKQLVEKFTIERVNKSGAIFDST---KLRWM---NGQH 377
LL D T + + T + + ++ ++ + S A+F + + + GQ
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKR-PFDKKSNS-ALFRAVGEGNAQLVAIFGGQG 164
Query: 378 LRAIPSNELTKLIGERWKS-TGILTESKGPFVDEAIQLLKD--------------GIDLV 422
EL L +++ ++ G + + + L + G++++
Sbjct: 165 NTDDYFEELRDL----YQTYHVLV----GDLIKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 423 ---------PDSDKALSNLLSYPL 437
PD D LS +S PL
Sbjct: 217 EWLENPSNTPDKDYLLSIPISCPL 240
Score = 37.7 bits (87), Expect = 0.008
Identities = 42/256 (16%), Positives = 69/256 (26%), Gaps = 124/256 (48%)
Query: 4 IVAATPWS------RIRTITKLELAPPIFLQSSVYYCKRR-RFSVAASLSTNTNKVDGQV 56
+V+ P S +R AP QS + + +R+ +FS
Sbjct: 378 VVSGPPQSLYGLNLTLRKAK----APSGLDQSRIPFSERKLKFSN--------------- 418
Query: 57 RVRFAP--SPTGNLHVGGARTALFN--YLFARSKGGKFVLRIEDTDLERSTKESEEAVLQ 112
RF P SP F+ L + + + +
Sbjct: 419 --RFLPVASP-------------FHSHLL----------------------VPASDLINK 441
Query: 113 DLSWLGLDWDEG----PGV-----GGDYGPYRQSERNSLYKQYADKLLESGHVYRCFCSN 163
DL + ++ P V G D + S+ ++ D ++
Sbjct: 442 DLVKNNVSFNAKDIQIP-VYDTFDGSDL----RVLSGSISERIVDCIIRL---------- 486
Query: 164 EELEKMKEIAKLKQLPPVYTGKWATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIR 223
PV W T T + L+ G P GG+ + L
Sbjct: 487 ----------------PVK---WETTTQFKATHILDFG-P---------GGASGLGVL-- 515
Query: 224 GEVSWNLDTLGDFVIM 239
N D G VI+
Sbjct: 516 --THRNKDGTGVRVIV 529
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription
factor 1, high mobility group box transcription factor
1, structural genomics; NMR {Homo sapiens}
Length = 87
Score = 33.5 bits (77), Expect = 0.018
Identities = 7/33 (21%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 383 SNELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+ ++ ++G+RWK + + + EA L
Sbjct: 45 NRAISVILGDRWKK---MKNEERRMYTLEAKAL 74
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 32.2 bits (74), Expect = 0.035
Identities = 15/33 (45%), Positives = 24/33 (72%), Gaps = 4/33 (12%)
Query: 383 SNELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+ EL+K++G+ WK+ LT + K PFV+EA +L
Sbjct: 30 NAELSKMLGKSWKA---LTLAEKRPFVEEAERL 59
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: a.21.1.1
Length = 90
Score = 32.7 bits (75), Expect = 0.037
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+ELT+L+ W L+E K + L
Sbjct: 49 SELTRLLARMWND---LSEKKKAKYKAREAAL 77
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX
domain, structural genomics, NPPSFA, riken structural
genomics/proteomics initiative; NMR {Mus musculus}
Length = 82
Score = 32.2 bits (74), Expect = 0.045
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
TK++ + W L K + D A +
Sbjct: 36 RGATKILADWWAV---LDPKEKQKYTDMAKEY 64
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of
chromatin subfamily...; structural DNA-binding protein
BRAF35, DNA-bending; NMR {Mus musculus}
Length = 92
Score = 32.0 bits (73), Expect = 0.079
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEA 411
E+TK++G W L + K ++DEA
Sbjct: 37 EITKMLGAEWSK---LQPAEKQRYLDEA 61
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX,
amphoterin, DNA/structural protein complex; NMR {Homo
sapiens} SCOP: a.21.1.1 a.21.1.1
Length = 159
Score = 32.9 bits (75), Expect = 0.092
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEAIQLLK 416
E++K +G +WK LTE+ K PF EA +L
Sbjct: 34 EISKQLGYQWKM---LTEAEKWPFFQEAQKLQA 63
Score = 32.9 bits (75), Expect = 0.095
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
++ K +GE W + K P+ +A +L
Sbjct: 118 DVAKKLGEMWNN---TAADDKQPYEKKAAKL 145
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG,
TCR-A, transcription factor; HET: DNA; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 86
Score = 31.4 bits (72), Expect = 0.093
Identities = 6/50 (12%), Positives = 19/50 (38%), Gaps = 10/50 (20%)
Query: 372 WMNGQHLRAIPSN------ELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+M + + + +++G RW + L+ + + + A +
Sbjct: 13 YMKEMRANVVAESTLKESAAINQILGRRWHA---LSREEQAKYYELARKE 59
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor,
SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP:
a.21.1.1 PDB: 1j47_A
Length = 85
Score = 31.0 bits (71), Expect = 0.12
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+E++K +G +WK LTE+ K PF EA +L
Sbjct: 33 SEISKQLGYQWKM---LTEAEKWPFFQEAQKL 61
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain,
activator, DNA-binding, NUC transcription; HET: DNA;
2.77A {Homo sapiens}
Length = 106
Score = 31.6 bits (72), Expect = 0.12
Identities = 15/33 (45%), Positives = 22/33 (66%), Gaps = 4/33 (12%)
Query: 383 SNELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+ EL+K +G+ W+ L ES K PFV+EA +L
Sbjct: 57 NAELSKTLGKLWRL---LNESEKRPFVEEAERL 86
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA
complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1
PDB: 1hrz_A*
Length = 76
Score = 31.0 bits (71), Expect = 0.12
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+E++K +G +WK LTE+ K PF EA +L
Sbjct: 33 SEISKQLGYQWKM---LTEAEKWPFFQEAQKL 61
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain,
endodermal, activator, DNA- nucleus, transcription
regulation, transcrip complex; HET: DNA; 2.75A {Mus
musculus} PDB: 2yul_A
Length = 83
Score = 31.0 bits (71), Expect = 0.14
Identities = 15/32 (46%), Positives = 23/32 (71%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
EL+K++G+ WK+ LT + K PFV+EA +L
Sbjct: 35 AELSKMLGKSWKA---LTLAEKRPFVEEAERL 63
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 31.1 bits (71), Expect = 0.14
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEA 411
E +K ERWK+ ++ KG F D A
Sbjct: 39 EFSKKCSERWKT---MSAKEKGKFEDMA 63
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 31.2 bits (71), Expect = 0.14
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEA 411
E +K ERWK+ ++ K F + A
Sbjct: 47 EFSKKCSERWKT---MSGKEKSKFDEMA 71
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition,
chromatin, DNA binding protein, DNA sequence specific,
testis determining.; NMR {Mus musculus} SCOP: a.21.1.1
Length = 81
Score = 30.6 bits (70), Expect = 0.15
Identities = 10/33 (30%), Positives = 21/33 (63%), Gaps = 4/33 (12%)
Query: 383 SNELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
++ ++K++G RWK+ +T K P+ +E +L
Sbjct: 32 NSNISKILGSRWKA---MTNLEKQPYYEEQARL 61
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A
1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A
Length = 77
Score = 30.7 bits (70), Expect = 0.16
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
++ K +GE W + K P+ +A +L
Sbjct: 36 DVAKKLGEMWNN---TAADDKQPYEKKAAKL 63
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation,
transcription-DNA CO; HET: DNA; 2.40A {Mus musculus}
Length = 79
Score = 30.6 bits (70), Expect = 0.18
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
E++K +G+RWK L +S K PF+ EA +L
Sbjct: 31 AEISKRLGKRWKL---LKDSDKIPFIQEAERL 59
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 30.3 bits (69), Expect = 0.19
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 376 QHLRAIPSNELTKLIGERWKSTGILTES-KGPFVDEA 411
Q + E K + E WK+ L++S K ++ A
Sbjct: 19 QEAKGDSPQEKLKTVKENWKN---LSDSEKELYIQHA 52
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT
DNA, protein-drug-DNA compl regulation-DNA complex; HET:
DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB:
1j3x_A
Length = 71
Score = 30.0 bits (68), Expect = 0.21
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 385 ELTKLIGERWKSTGILTESKGPFVDEA 411
E +K ERWK+ + KG F D A
Sbjct: 33 EFSKKCSERWKTMS--AKEKGKFEDMA 57
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 30.5 bits (69), Expect = 0.22
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 385 ELTKLIGERWKSTGILTESKGPFVDEAIQLLK 416
+ T I E WK+ E K + ++A + L+
Sbjct: 37 DATLQIEELWKTLS--EEEKLKYEEKATKDLE 66
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 30.8 bits (70), Expect = 0.23
Identities = 7/32 (21%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 381 IPSNELTKLIGERWKSTGILTES-KGPFVDEA 411
+ + +LTK++ +++K L E K ++ +
Sbjct: 36 MSNLDLTKILSKKYKE---LPEKKKMKYIQDF 64
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 30.4 bits (69), Expect = 0.24
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+ K+IG W + L++ K P+ + +
Sbjct: 54 AIGKMIGAAWNA---LSDEEKKPYERMSDED 81
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus
musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B
Length = 80
Score = 30.2 bits (69), Expect = 0.26
Identities = 14/32 (43%), Positives = 22/32 (68%), Gaps = 4/32 (12%)
Query: 384 NELTKLIGERWKSTGILTES-KGPFVDEAIQL 414
+E++K +G WK L+E+ K PF+DEA +L
Sbjct: 31 SEISKRLGAEWKL---LSETEKRPFIDEAKRL 59
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A
1qrv_A*
Length = 73
Score = 29.9 bits (68), Expect = 0.27
Identities = 7/30 (23%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 385 ELTKLIGERWKSTGILTESKGPFVDEAIQL 414
E+ K GE W++ + + K + +A +
Sbjct: 33 EVAKRGGELWRA---MKD-KSEWEAKAAKA 58
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 29.6 bits (67), Expect = 0.30
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 4/27 (14%)
Query: 385 ELTKLIGERWKSTGILTESKGPFVDEA 411
E+ K GE WK L + K + D A
Sbjct: 33 EIAKKGGEMWKE---LKD-KSKWEDAA 55
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI;
NMR {Mus musculus} SCOP: a.21.1.1
Length = 108
Score = 30.7 bits (69), Expect = 0.32
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 376 QHLRAIPSNELTKLIGERWKSTGILTES-KGPFVDEAIQLLKD 417
+++ +PS E L ++WK L++ K + + Q KD
Sbjct: 34 ANMKDVPSTERMVLCSQQWKL---LSQKEKDAYHKKCDQKKKD 73
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 29.7 bits (67), Expect = 0.48
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 4/28 (14%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEA 411
E++K++ W L E K + +
Sbjct: 47 EVSKIVASMWDG---LGEEQKQVYKKKT 71
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1
Length = 101
Score = 29.9 bits (67), Expect = 0.53
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 372 WMNGQHLRAIPSNELTKLIGERWKSTGILTES-KGPFVDEAIQLLK 416
++ L +P E IG RW+ +++S K + A + +
Sbjct: 23 LLSNGELNHLPLKERMVEIGSRWQR---ISQSQKEHYKKLAEEQQR 65
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A
1lwm_A
Length = 93
Score = 29.6 bits (67), Expect = 0.54
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEA 411
++ K +GE+WK+ LT K P+ +A
Sbjct: 50 QVGKKLGEKWKA---LTPEEKQPYEAKA 74
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group,
transcription, LSP1, mitochon transcription-DNA complex;
HET: DNA; 2.50A {Homo sapiens}
Length = 238
Score = 31.0 bits (69), Expect = 0.74
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 376 QHLRAIPSNELTKLIGERWKSTGILTES-KGPFVDEAIQLLK 416
Q + E K + E WK+ L++S K ++ A +
Sbjct: 163 QEAKGDSPQEKLKTVKENWKN---LSDSEKELYIQHAKEDET 201
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.3 bits (67), Expect = 0.74
Identities = 7/22 (31%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 410 EAIQLLKDGIDL-VPDSDKALS 430
+A++ L+ + L DS AL+
Sbjct: 20 QALKKLQASLKLYADDSAPALA 41
Score = 28.0 bits (61), Expect = 3.9
Identities = 5/27 (18%), Positives = 14/27 (51%), Gaps = 9/27 (33%)
Query: 14 RTITKLE--L-------APPIFLQSSV 31
+ + KL+ L AP + +++++
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATM 46
>1j5p_A Aspartate dehydrogenase; TM1643, structural genomics, JCSG, protein
structure initiative, joint center for structural G
oxidoreductase; HET: NAD; 1.90A {Thermotoga maritima}
SCOP: c.2.1.3 d.81.1.3 PDB: 1h2h_A*
Length = 253
Score = 30.4 bits (68), Expect = 1.0
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 10/71 (14%)
Query: 41 VAASLSTNTNKVDGQVRVRFAPSPTGNLHVGGARTALFNYLFARSKGGKFVLRIEDTDLE 100
VA+++ +V + P+ N+H+ + S G + +IE+
Sbjct: 177 VASTIGLIVGFEKVKVTIVADPAMDHNIHI----------VRISSAIGNYEFKIENIPSP 226
Query: 101 RSTKESEEAVL 111
+ K S V
Sbjct: 227 ENPKTSMLTVY 237
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding,
helix-turn-helix motif, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 173
Score = 30.0 bits (67), Expect = 1.2
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 385 ELTKLIGERWKSTGILTES-KGPFVDEAIQLLK 416
++ K +GE W + K P+ +A +L +
Sbjct: 131 DVAKKLGEMWNN---TAADDKQPYEKKAAKLKE 160
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 29.3 bits (65), Expect = 2.2
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 4/40 (10%)
Query: 378 LRAIPSNELTKLIGERWKSTGILTES-KGPFVDEAIQLLK 416
+ E K + E WK+ L++S K ++ A +
Sbjct: 133 AKGDSPQEKLKTVKENWKN---LSDSEKELYIQHAKEDET 169
>2ho3_A Oxidoreductase, GFO/IDH/MOCA family; streptococcus pneumonia
reductive methylation, structural genomics, PSI-2,
protein initiative; HET: MLY; 2.00A {Streptococcus
pneumoniae} PDB: 2ho5_A
Length = 325
Score = 29.3 bits (66), Expect = 2.3
Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 140 NSLYKQYADKLLESG-HVYRC---FCSN-EELEKMKEIAKLKQL 178
NSL+ A L +G HV S +E + + A+
Sbjct: 72 NSLHFAQAKAALSAGKHVI-LEKPAVSQPQEWFDLIQTAEKNNC 114
>2or0_A Hydroxylase; APC7385, rhodococcus SP. RHA1, structu genomics,
PSI-2, protein structure initiative, midwest CENT
structural genomics, MCSG; HET: MSE; 2.10A {Rhodococcus
SP}
Length = 414
Score = 29.3 bits (66), Expect = 2.8
Identities = 21/113 (18%), Positives = 38/113 (33%), Gaps = 16/113 (14%)
Query: 186 WATATDAEVQKELERGTPYTYRFRVPKGGSLKISDLIRGEVSWNLDTLGDFVIMRSNGQP 245
WA E TP + +P+ + D +W D +G +R G
Sbjct: 163 WAFLGAMVGDGEGGIATPSSLHVILPRTDYQIVED------TW--DVIG----LRGTG-- 208
Query: 246 VYNFCVTVDDATMAISHVIRAEEHLPNTLRQALIYKALGFSMPYFAHVSLILA 298
+ + VD A + + A + + ++ F+MPY L +
Sbjct: 209 --SKDLIVDGAFVPGYRTLNAAKVMDGRAQKEAGRPEPLFNMPYSCMFPLGIT 259
>1w0m_A TIM, triosephosphate isomerase; glycolysis, gluconeogenesis; 2.5A
{Thermoproteus tenax} SCOP: c.1.1.1
Length = 226
Score = 28.7 bits (65), Expect = 2.8
Identities = 13/68 (19%), Positives = 19/68 (27%), Gaps = 12/68 (17%)
Query: 137 SERNSLYKQYAD---KLLESGHVYRCFCSNEELEKMKEIAKLKQL-----PP--VYTGKW 186
SE A K G + C+ + A L PP + TG+
Sbjct: 94 SEAPLKLNDLARLVAKAKSLG-LDVVVCAPDPRTS-LAAAALGPHAVAVEPPELIGTGRA 151
Query: 187 ATATDAEV 194
+ E
Sbjct: 152 VSRYKPEA 159
>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha
helix, antivirus, antiviral protein; 2.80A {Homo
sapiens}
Length = 472
Score = 29.1 bits (65), Expect = 3.2
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 409 DEAIQLLKDGIDLVPDSDKALSNL 432
D+AI+LLK ++ +P++ +
Sbjct: 264 DKAIELLKKALEYIPNNAYLHCQI 287
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 5.0
Identities = 12/91 (13%), Positives = 25/91 (27%), Gaps = 43/91 (47%)
Query: 89 KFVLRIEDTDLERSTKESE--EAVLQDLSWLGLDWDEGPGVGGDYGPYRQSERNSLYKQY 146
+ R+++ D E E E +DL +W ++
Sbjct: 93 EQRKRLQELDAASKVMEQEWREKAKKDLE----EW---------------------NQRQ 127
Query: 147 ADKLLESGHVYRCFCSNEELEKMKEIAKLKQ 177
+E++EK K ++
Sbjct: 128 ----------------SEQVEKNKINNRIAD 142
>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc
genomics, protein structure initiative; 2.20A
{Campylobacter jejuni}
Length = 464
Score = 28.3 bits (64), Expect = 5.0
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 64 PTGNLHVGGARTALF 78
PTG LH+G AR A+F
Sbjct: 41 PTGPLHIGHARGAVF 55
>3bw2_A 2-nitropropane dioxygenase; TIM barrel, oxidoreductase; HET: FMN;
2.10A {Streptomyces ansochromogenes} PDB: 3bw4_A*
3bw3_A*
Length = 369
Score = 28.1 bits (63), Expect = 5.7
Identities = 9/31 (29%), Positives = 12/31 (38%)
Query: 392 ERWKSTGILTESKGPFVDEAIQLLKDGIDLV 422
R + G LT +EA + G D V
Sbjct: 139 ARLRRAGTLTLVTATTPEEARAVEAAGADAV 169
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 28.0 bits (62), Expect = 6.6
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 382 PSNELTKLIGERWKSTGILTESKGPFVDEAIQLLKDG 418
PS E+ + + ++ E+K +E ++L+K G
Sbjct: 392 PSYEMLESVRIHLSGIPVIEENKKTRHEEVLELMKTG 428
>3ldh_A Lactate dehydrogenase; oxidoreductase, CHOH donor, NAD acceptor;
HET: NAD; 3.00A {Squalus acanthias} SCOP: i.12.1.1
Length = 330
Score = 27.6 bits (62), Expect = 7.5
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 356 ERVNKSGAIFDSTKLRWMNGQHLRAIPSNELTKLIGE 392
R+ SG DS + R++ G+ L + +IG+
Sbjct: 157 HRIIGSGCNLDSARFRYLMGERLGVHSCLVIGWVIGQ 193
>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein
O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB:
2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*
Length = 568
Score = 27.9 bits (62), Expect = 8.1
Identities = 5/28 (17%), Positives = 11/28 (39%)
Query: 408 VDEAIQLLKDGIDLVPDSDKALSNLLSY 435
+ A L+P+ + LL++
Sbjct: 107 AEAAAAAYTRAHQLLPEEPYITAQLLNW 134
>2h6r_A Triosephosphate isomerase; beta-alpha barrel; 2.30A
{Methanocaldococcus jannaschii}
Length = 219
Score = 27.2 bits (61), Expect = 8.4
Identities = 15/68 (22%), Positives = 21/68 (30%), Gaps = 12/68 (17%)
Query: 137 SERNSLYKQYAD---KLLESGHVYRCFCSNEELEKMKEIAKLKQLP----PVY---TGKW 186
SE+ L K G + C+N K +A L P TG
Sbjct: 91 SEKRMLLADIEAVINKCKNLG-LETIVCTNNINTS-KAVAALSPDCIAVEPPELIGTGIP 148
Query: 187 ATATDAEV 194
+ + EV
Sbjct: 149 VSKANPEV 156
>1j0a_A 1-aminocyclopropane-1-carboxylate deaminase; PLP dependent, lyase;
HET: PLP; 2.50A {Pyrococcus horikoshii} SCOP: c.79.1.1
PDB: 1j0b_A*
Length = 325
Score = 27.7 bits (61), Expect = 8.7
Identities = 7/24 (29%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 164 EELEKMKEIAKLKQLP--PVYTGK 185
E + ++++ + + PVYTGK
Sbjct: 262 EVAQIIRKVGTREGIILDPVYTGK 285
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
0.318 0.135 0.402
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,884,154
Number of extensions: 419576
Number of successful extensions: 1582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1543
Number of HSP's successfully gapped: 78
Length of query: 443
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 346
Effective length of database: 3,993,456
Effective search space: 1381735776
Effective search space used: 1381735776
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 (21.7 bits)
S2: 59 (26.4 bits)