RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780573|ref|YP_003064986.1| cysteinyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (461 letters) >gnl|CDD|30564 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 464 Score = 523 bits (1348), Expect = e-149 Identities = 212/485 (43%), Positives = 283/485 (58%), Gaps = 49/485 (10%) Query: 4 KIKIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGE 63 +K+YNTL R+ EF IDP ++MYVCGPTVYD+AHIG+AR +VFDVL R LRY + Sbjct: 1 MLKLYNTLTRQKEEFVPIDPGKVKMYVCGPTVYDYAHIGHARTYVVFDVLRRYLRYLGYK 60 Query: 64 KCVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQP 123 VTYVRNITDIDDKII RAR+E SI + + F +D L L P +P Sbjct: 61 --VTYVRNITDIDDKIINRAREEGLSI------REVAERYIAAFFEDMDALNVLPPDIEP 112 Query: 124 RATNHIPQMIYLIQNIILHGHAYEA-NNEIIFDTSSIPNYGSFSRR-KIDEQKMGTRVPE 181 RAT HI ++I I+ +I G+AY A + ++ FD S +YG S R ++E + G RV Sbjct: 113 RATEHIDEIIEFIEKLIEKGYAYVADDGDVYFDVSKFKDYGKLSGRDSLEELQAGARVEV 172 Query: 182 KYHKKNPADFILWKRSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLDLI 241 K+NP DF+LWK + P EP W+SPWG+GRPGWHIECSAMS+ YLG+ FDIHGGG DLI Sbjct: 173 DEEKRNPLDFVLWKAAKPGEPSWDSPWGKGRPGWHIECSAMSTKYLGETFDIHGGGSDLI 232 Query: 242 FPHHENEIAQSCCADRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRS 301 FPHHENEIAQS A ++ A W+HNGFLN++G KMSKS GNFIT+ +LL+ Sbjct: 233 FPHHENEIAQSEAATGVKPFAKYWMHNGFLNIDGEKMSKSLGNFITVRDLLKK------- 285 Query: 302 WPAPVIRLAMLMTHYREPIDFTVQRLTEAEILLSKWPQT---------STSKGIIDP--- 349 + V+RL +L +HYR P+DF+ + L EA+ L + + Sbjct: 286 YDPEVLRLFLLSSHYRSPLDFSEELLEEAKKALERLYNALRRLRDLAGDAELADLKEFEA 345 Query: 350 AVLSALYNDLNTVSAIQALHKLARESTKNHD--------LLPIFNASAHILGIEVCKEHL 401 AL +D NT A+ L +LA+E + + +L A ILG++V Sbjct: 346 RFREALDDDFNTPKALAVLFELAKEINRLLEEGKSDAKAVLSALKALLAILGLKVLGLFP 405 Query: 402 N------KNISIAIEKLVQERLILLKMKKFSSADYIRKQLESKGFILEDYKNPDNGQRMT 455 ++ IE L++ERL K K ++ AD IR +L + G ILED + T Sbjct: 406 QSGAQEDESDDEEIEALIEERLEARKAKNWALADEIRDELLALGIILEDTPDG------T 459 Query: 456 RWKQK 460 W++K Sbjct: 460 TWRRK 464 >gnl|CDD|37218 KOG2007, KOG2007, KOG2007, Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 586 Score = 373 bits (958), Expect = e-104 Identities = 178/497 (35%), Positives = 251/497 (50%), Gaps = 59/497 (11%) Query: 1 MKKKIKIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYY 60 ++K+YN+L R+ F + + + Y+CGPTVYD +H+G+AR + FD+L R+LR Y Sbjct: 31 QPTELKLYNSLTRQKEVFIPNNGNKVTWYICGPTVYDSSHMGHARSYVSFDILRRILRDY 90 Query: 61 YGEKCVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPT 120 +G VT+V NITD+DDKII+RAR+E +S ++F++D L L PT Sbjct: 91 FGYD-VTFVMNITDVDDKIIKRARKEEMGEKPLS-LSERFCYYEEEFLQDMAALNVLPPT 148 Query: 121 HQPRATNHIPQMIYLIQNIILHGHAYEANNEIIFDTSSIP-NYGSFSRRKIDEQKMGTRV 179 Q R + ++PQ+I IQ II +G+AY + + FD P +YG ++ + Q+ G V Sbjct: 149 VQTRVSEYVPQIIKFIQKIIDNGYAYAVDGSVYFDVDKFPHSYGKLVGQRKNLQE-GEGV 207 Query: 180 PEKYHKKNPADFILWKRSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLD 239 K++PADF LWK S P EP WESPWG+GRPGWHIECSAM+S LG DIHGGG+D Sbjct: 208 LSDSRKRSPADFALWKASKPGEPSWESPWGKGRPGWHIECSAMASAILGSQLDIHGGGID 267 Query: 240 LIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGG 299 L FPHHENEIAQS A + N ++H G L + G KMSKS NFITI E L KK+ Sbjct: 268 LAFPHHENEIAQSEAAFDDSQWVNYFLHTGHLTINGEKMSKSLKNFITIKEAL--KKYSP 325 Query: 300 RSWPAPVIRLAMLMTHYREPIDFTVQRLTEAEILLS----------------KWPQTSTS 343 R +RLA L+ +R P+D++ + +A L K + + Sbjct: 326 R-----QLRLAFLLHQWRSPLDYSDSTMEQALQLEKSLNNFFLDVKALLRGAKPFEKLSE 380 Query: 344 K--------GIIDPAVLSALYNDLNTVSAIQALHKL---------ARESTKNHDLLPIFN 386 K G AV +AL ++ +T ++A+ +L N LL Sbjct: 381 KEAELLEDFGKTQTAVHAALCDNFDTPRVMEAIRELVSQGNAYIRESGERPNSALLKAIA 440 Query: 387 AS----AHILGIEVCKE---------HLNKNISIAIEKLVQERLILLKMKKFSSA-DYIR 432 + I G+ K + V+E K+ + D +R Sbjct: 441 SYITKLLKIFGLSEGKGQQYVLEATVMPYVQSLSEFREKVREVAREKKVPEILELCDTLR 500 Query: 433 -KQLESKGFILEDYKNP 448 L G LED K Sbjct: 501 DSDLLELGVRLEDRKGS 517 >gnl|CDD|110410 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic domain. This family includes only cysteinyl tRNA synthetases. Length = 301 Score = 372 bits (957), Expect = e-103 Identities = 145/315 (46%), Positives = 197/315 (62%), Gaps = 17/315 (5%) Query: 17 EFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGEKCVTYVRNITDID 76 F + + MYVCGPTVYD +HIG+AR + FDVL R L+ + V +V+N TDID Sbjct: 1 FFVPLHQGKVNMYVCGPTVYDDSHIGHARSAVAFDVLRRYLQALGYD--VQFVQNFTDID 58 Query: 77 DKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQPRATNHIPQMIYLI 136 DKII+RA+Q+ S + ++ + KD L L P +PR T HI ++I I Sbjct: 59 DKIIKRAQQQGESFRE------LAARFITAYTKDMDALNVLPPDLEPRVTEHIDEIIEFI 112 Query: 137 QNIILHGHAYEA-NNEIIFDTSSIPNYGSFSRRKIDEQKMGTRVPEKYHKKNPADFILWK 195 + +I G+AY + N ++ FD SS P+YG S + +++ + G R K++P DF LWK Sbjct: 113 ERLIKKGYAYVSDNGDVYFDVSSFPDYGKLSGQNLEQLEAGARGEVGEGKRDPLDFALWK 172 Query: 196 RSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCA 255 S EP W+SPWG+GRPGWHIECSAM+ YLG DIHGGG+DL FPHHENEIAQS A Sbjct: 173 ASKEGEPSWDSPWGKGRPGWHIECSAMARKYLGSQIDIHGGGVDLKFPHHENEIAQSEAA 232 Query: 256 DRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTH 315 + A W+HNG L +EG KMSKS GNF+TI ++L K++ R ++R +L H Sbjct: 233 FDQQ-LAKYWLHNGHLMIEGEKMSKSLGNFLTIRDVL--KRYDPR-----ILRYFLLSVH 284 Query: 316 YREPIDFTVQRLTEA 330 YR P+DF+ + L +A Sbjct: 285 YRSPLDFSEELLEQA 299 >gnl|CDD|173899 cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Length = 213 Score = 174 bits (443), Expect = 5e-44 Identities = 63/109 (57%), Positives = 78/109 (71%), Gaps = 8/109 (7%) Query: 215 WHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE 274 WHIECSAM+ YLG+ FDIHGGG+DLIFPHHENEIAQS A + A W+H G L ++ Sbjct: 113 WHIECSAMAMKYLGETFDIHGGGVDLIFPHHENEIAQSEAA-TGKPFARYWLHTGHLTID 171 Query: 275 GRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDFT 323 G KMSKS GNFIT+ + L KK+ V+RLA+L +HYR P+DF+ Sbjct: 172 GEKMSKSLGNFITVRDAL--KKYDPE-----VLRLALLSSHYRSPLDFS 213 Score = 151 bits (385), Expect = 3e-37 Identities = 59/125 (47%), Positives = 77/125 (61%), Gaps = 11/125 (8%) Query: 6 KIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYY-YGEK 64 ++YNTL R+ EF ++P + MYVCGPTVYD+AHIG+AR +VFDVL R L Y Sbjct: 1 RLYNTLTRQKEEFVPLNPGLVTMYVCGPTVYDYAHIGHARTYVVFDVLRRYLEDLGYK-- 58 Query: 65 CVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQPR 124 V YV+NITDIDDKII+RAR+E + + + T++F +D L L P PR Sbjct: 59 -VRYVQNITDIDDKIIKRAREEG--LSWKE----VADYYTKEFFEDMKALNVLPPDVVPR 111 Query: 125 ATNHI 129 HI Sbjct: 112 VW-HI 115 >gnl|CDD|153417 cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA. Length = 156 Score = 56.8 bits (138), Expect = 1e-08 Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 16/108 (14%) Query: 353 SALYNDLNTVSAIQALHKLARE----STKNHDLLPIFNAS----AHILGI--EVCKEHLN 402 +A+ +D NT A+ L +LARE ++ + A +LG+ + + L Sbjct: 40 AAMDDDFNTPEALAVLFELAREINRLKKEDIEKAAALAALLKALGGVLGLLQQDPEAFLQ 99 Query: 403 KNISI------AIEKLVQERLILLKMKKFSSADYIRKQLESKGFILED 444 IE L+ +R K K ++ AD IR +L ++G ILED Sbjct: 100 GGTGEGGLSVAEIEALIAQRNQARKAKDWAEADRIRDELAAQGIILED 147 >gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Length = 143 Score = 51.7 bits (124), Expect = 4e-07 Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 4/69 (5%) Query: 214 GWHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNL 273 + +A DIH GG D + H E + A + G + Sbjct: 77 EYMFLQAADFLLLYETECDIHLGGSDQLG-HIELGLELLKKAGG--PARPFGLTFGRVMG 133 Query: 274 E-GRKMSKS 281 G KMSKS Sbjct: 134 ADGTKMSKS 142 Score = 47.9 bits (114), Expect = 7e-06 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%) Query: 28 MYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGEKCVTYVRNITDIDDKIIERA 83 G T + HIG+ R ++ FD L + R + V + I D I + A Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYK--VRCIALIDDAGGLIGDPA 54 >gnl|CDD|30409 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 933 Score = 46.7 bits (111), Expect = 1e-05 Identities = 35/132 (26%), Positives = 63/132 (47%), Gaps = 17/132 (12%) Query: 266 IHNGF-LNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDFTV 324 + +GF L+ +GRKMSKS GN + +++ K+G A ++RL + + Y E + F+ Sbjct: 590 LTHGFVLDEKGRKMSKSLGNVVDPQDVI--DKYG-----ADILRLWVASSDYWEDLRFSD 642 Query: 325 QRLTEAEILLSKWPQT----STSKGIIDPAVLSALYNDLNT-----VSAIQALHKLARES 375 + L + + K T + DP + L +L +S + +L K RE+ Sbjct: 643 EILKQVREVYRKIRNTYRFLLGNLDDFDPKKDAVLPEELRELDRWILSRLNSLVKEVREA 702 Query: 376 TKNHDLLPIFNA 387 +N+D + A Sbjct: 703 YENYDFHKVVRA 714 >gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 314 Score = 45.7 bits (109), Expect = 3e-05 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 7/47 (14%) Query: 266 IHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML 312 I G + LEG KMSKS GN +T +E + KK+G A RL +L Sbjct: 264 IVQGMVLLEGEKMSKSKGNVVTPDEAI--KKYG-----ADAARLYIL 303 >gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function. Length = 319 Score = 43.3 bits (103), Expect = 1e-04 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 7/46 (15%) Query: 268 NGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLM 313 +G+L +EG+KMSKS GN + ++LLE + A +R +L Sbjct: 271 HGYLTVEGKKMSKSRGNVVDPDDLLER-------YGADALRYYLLR 309 >gnl|CDD|30492 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 558 Score = 42.6 bits (100), Expect = 2e-04 Identities = 17/27 (62%), Positives = 21/27 (77%) Query: 268 NGFLNLEGRKMSKSNGNFITINELLET 294 +GFL LEG+KMSKS GN + +ELLE Sbjct: 324 HGFLTLEGQKMSKSRGNVVDPDELLEQ 350 Score = 28.7 bits (64), Expect = 3.7 Identities = 8/26 (30%), Positives = 11/26 (42%) Query: 33 PTVYDFAHIGNARPMIVFDVLYRLLR 58 P H+G+ + DV R LR Sbjct: 14 PYPNGPPHLGHLYTYLAADVYARYLR 39 >gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function. Length = 312 Score = 41.3 bits (97), Expect = 6e-04 Identities = 55/303 (18%), Positives = 92/303 (30%), Gaps = 56/303 (18%) Query: 33 PTVYDFAHIGNARPMIVFDVL--YRLLRYYY----------GEKCVTYVRNITDIDDKII 80 P H+G+A I+ D + Y+ +R Y G K I Sbjct: 9 PYANGSLHLGHALTHIIADFIARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKTI 68 Query: 81 ERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAP------THQPRATNHIPQMIY 134 + + + + +D RL T +P + + Sbjct: 69 WIEE-------FREDPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPE---YSKAVEL 118 Query: 135 LIQNIILHGHAYEANNEIIFDTSSIPNYGSFSRRKIDEQKMGTRVPEKYHKKNPA---DF 191 + + G Y + + + F + + + G VPE + A Sbjct: 119 IFSRLYEKGLIYRGTHPVRITEQWFFDMPKFKEKLLKALRRGKIVPEHVKNRMEAWLESL 178 Query: 192 ILWKRSTPMEPGWESPWGRGRPGWHIEC-------SAMSSHYL--GKVF------DIHGG 236 + W S WG P + S Y + F D H Sbjct: 179 LDWAISRQR------YWGTPLPEDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYPADWHLI 232 Query: 237 GLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE-GRKMSKSNGNFITINELLETK 295 G D++ I N+ +H GF+ E G+KMSKS GN I ++++E Sbjct: 233 GKDILRGWANFWITMLVALFGEIPPKNLLVH-GFVLDEGGQKMSKSKGNVIDPSDVVE-- 289 Query: 296 KFG 298 K+G Sbjct: 290 KYG 292 >gnl|CDD|35658 KOG0437, KOG0437, KOG0437, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 1080 Score = 37.3 bits (86), Expect = 0.008 Identities = 17/31 (54%), Positives = 21/31 (67%), Gaps = 2/31 (6%) Query: 268 NGFLNLEGRKMSKSNGNFITINELLETKKFG 298 NG L L KMSKS GNF+T+ + +E KFG Sbjct: 701 NGHLMLNSEKMSKSTGNFMTLEQAIE--KFG 729 >gnl|CDD|30871 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 877 Score = 36.0 bits (83), Expect = 0.023 Identities = 32/135 (23%), Positives = 60/135 (44%), Gaps = 13/135 (9%) Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAM-LMTHYREPID 321 +++IH + +GRKMSKS GN I ++++ K+G A +R + + I+ Sbjct: 511 DVYIHGLVRDEQGRKMSKSKGNVIDPLDVID--KYG-----ADALRFTLASLASPGRDIN 563 Query: 322 FTVQRLTEAEILLSK-WPQTSTSKGIIDPAVLSALYNDLNTVSA---IQALHKLARESTK 377 F +R+ L+K W T +D L +++ + L++ +E T+ Sbjct: 564 FDEKRVEGYRNFLNKLWNATRFVLMNLDDLGPDDLDLLALSLADRWILSRLNETVKEVTE 623 Query: 378 NHDLLPIFNASAHIL 392 D F+ +A L Sbjct: 624 ALDNYR-FDEAARAL 637 >gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 577 Score = 35.6 bits (82), Expect = 0.032 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 18/92 (19%) Query: 258 IEKTANIWIHNGF---LNLEGRKMSKSNGNFITINELLE----------TKKFGGRSWPA 304 + +H G EG KMS GN +T+++LL+ +K A Sbjct: 361 YGPDKEVLLHQGVGLVRGGEGVKMSTRAGNVVTLDDLLDEAGERAPEEMEEKEEKNEEIA 420 Query: 305 PV-----IRLAMLMTHYREPIDFTVQRLTEAE 331 V +R A L + F + E Sbjct: 421 EVVGIDAVRYADLSRSRDKDYVFDWDKALSFE 452 Score = 27.1 bits (60), Expect = 9.4 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 40 HIGNARPMIVFDVLYRLLRYY 60 HIG+ R I+ D L R+L + Sbjct: 133 HIGHLRNAIIGDSLARILEFL 153 >gnl|CDD|145212 pfam01921, tRNA-synt_1f, tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes. Length = 355 Score = 34.5 bits (80), Expect = 0.064 Identities = 14/24 (58%), Positives = 14/24 (58%) Query: 270 FLNLEGRKMSKSNGNFITINELLE 293 L G KMS S GN ITI E LE Sbjct: 271 ILLKGGGKMSSSKGNGITIEEWLE 294 >gnl|CDD|30841 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 814 Score = 34.5 bits (79), Expect = 0.065 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 8/48 (16%) Query: 266 IHNGF-LNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML 312 I G L EG KMSKS GN + E +E K+G A +RL ++ Sbjct: 567 ITQGMVLGEEGEKMSKSKGNVVDPEEAVE--KYG-----ADTVRLYIM 607 >gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 382 Score = 33.8 bits (78), Expect = 0.12 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 7/51 (13%) Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLM 313 +++H + +GRKMSKS GN I ++++ +G A +R + Sbjct: 329 EVYLHGLVRDEDGRKMSKSLGNVIDPLDVID--GYG-----ADALRFTLAS 372 >gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity. Length = 353 Score = 33.1 bits (76), Expect = 0.18 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 11/64 (17%) Query: 270 FLNLEGR-KMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML---MTHYREPIDFTVQ 325 F+ L+G KMS S GN IT ++ LE P V+R D + Sbjct: 267 FIGLKGGGKMSSSKGNVITPSDWLEV-------APPEVLRYLYARRKNPEKHIGFDLDIL 319 Query: 326 RLTE 329 RL + Sbjct: 320 RLYD 323 >gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. Length = 338 Score = 32.6 bits (75), Expect = 0.25 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 8/50 (16%) Query: 266 IHNGFLNLE-GRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMT 314 I +GF+ E GRKMSKS GN++ E+++ K+G A +RL + + Sbjct: 287 IVHGFVLDEDGRKMSKSLGNYVDPQEVVD--KYG-----ADALRLWVASS 329 >gnl|CDD|143905 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included. Length = 606 Score = 32.3 bits (74), Expect = 0.27 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 7/54 (12%) Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHY 316 N+ +H + +GRKMSKS GN I+ L K+G A +RL + + Y Sbjct: 553 NVLVHGLVRDEQGRKMSKSLGN--VIDPLDVIDKYG-----ADALRLWLASSDY 599 >gnl|CDD|31574 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]. Length = 521 Score = 30.2 bits (68), Expect = 1.3 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 8/54 (14%) Query: 270 FLNLEGR-KMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDF 322 ++ L+G KMS S GN I++++ LE P V+R + T IDF Sbjct: 269 WILLKGGGKMSSSKGNVISLSDWLEV-------APPEVLRYLIARTKPNRHIDF 315 >gnl|CDD|36247 KOG1029, KOG1029, KOG1029, Endocytic adaptor protein intersectin [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 1118 Score = 30.1 bits (67), Expect = 1.5 Identities = 12/29 (41%), Positives = 15/29 (51%) Query: 187 NPADFILWKRSTPMEPGWESPWGRGRPGW 215 P D I+ S EPGW + RG+ GW Sbjct: 713 EPGDIIIVFESQAAEPGWLAGELRGKTGW 741 >gnl|CDD|114364 pfam05636, DUF795, Protein of unknown function (DUF795). This family consists of several bacterial proteins of unknown function. Length = 389 Score = 29.7 bits (67), Expect = 2.0 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%) Query: 388 SAHILGIEVCK--EHLNKNIS-IAIEKLVQERLILLKMKKFSSADYIRKQLESKG 439 +ILG+E K + NI I++ L +F+SA IRK L+ K Sbjct: 161 PNNILGLEYAKAIKKAGSNIKLYTIKREGAGYHDLELEDQFASATAIRKALKEKD 215 >gnl|CDD|35654 KOG0433, KOG0433, KOG0433, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 937 Score = 29.2 bits (65), Expect = 2.3 Identities = 30/164 (18%), Positives = 61/164 (37%), Gaps = 21/164 (12%) Query: 264 IWIHNGFLNLEGRKMSKSNGNFIT----INELLETKKFGGRSWPAPVIRLAMLMTHYREP 319 + +H L+ G KMSKS GN + + L+ +G A +R + + Sbjct: 600 VIVHGFTLDENGNKMSKSLGNVVDPTMVTDGSLKQPAYG-----ADGLRFWVAGSENTGE 654 Query: 320 IDFTVQRLTEAEILLSKWPQTST-SKGII---DPAVLSALYNDLNTVS--AIQALHKLAR 373 + L + + L K+ T G + D + DL + +Q L + + Sbjct: 655 SKIGPKILDQVDEKLIKFRNTFRFLLGNLQDFDGKQVKFPLKDLRYIDQYMLQQLDAIVK 714 Query: 374 ESTKNHDLLPIFNASAHILGIEVCKEHLNKNISIAIEKLVQERL 417 + ++ + ++ L +N+S +V++RL Sbjct: 715 RIIELYNDYKFRKVVNDL------QQFLQRNLSAFYFDIVKDRL 752 >gnl|CDD|111812 pfam02964, MeMO_Hyd_G, Methane monooxygenase, hydrolase gamma chain. Length = 160 Score = 28.7 bits (64), Expect = 3.1 Identities = 12/25 (48%), Positives = 19/25 (76%) Query: 409 IEKLVQERLILLKMKKFSSADYIRK 433 IE+ ++E+L +LK +KF+ AD I K Sbjct: 51 IERKIEEKLAVLKTEKFNVADLITK 75 >gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal transduction mechanisms]. Length = 382 Score = 28.8 bits (64), Expect = 3.3 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 7/53 (13%) Query: 342 TSKGIIDPAVLSALYNDLNTVSAIQALHKLARESTKNHDLLPIFNASAHILGI 394 T KGI+ V++ + A++ + +LA E LP+ +A+ ++GI Sbjct: 316 TVKGIMTTPVVTVRPDT----PAVELVPRLADEG---LHALPVLDAAGKLVGI 361 >gnl|CDD|35653 KOG0432, KOG0432, KOG0432, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 995 Score = 28.7 bits (64), Expect = 3.8 Identities = 10/13 (76%), Positives = 10/13 (76%) Query: 274 EGRKMSKSNGNFI 286 GRKMSKS GN I Sbjct: 590 HGRKMSKSLGNVI 602 >gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H. Length = 370 Score = 28.0 bits (63), Expect = 5.1 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 3/57 (5%) Query: 219 CSAMSSHYLGKVFDI-HGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE 274 AM+ H LG ++ I HG ++ PH A++ ++ A + + Sbjct: 254 VHAMA-HPLGALYHIPHGLANAILLPHVMRFNAEA-IPEKYADIARAMGKVSGGSDD 308 >gnl|CDD|173969 cd08148, RuBisCO_large, Ribulose bisphosphate carboxylase large chain. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. Length = 366 Score = 27.8 bits (62), Expect = 7.0 Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%) Query: 49 VFDVLYRLLRYYYGEKCVTYVRNITDIDDKIIERA 83 V L R+ + GEK + V N+T +IIERA Sbjct: 181 VAAALDRV-QEETGEKKLYAV-NVTAGTFEIIERA 213 >gnl|CDD|32162 COG1979, COG1979, Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]. Length = 384 Score = 27.5 bits (61), Expect = 7.8 Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 5/38 (13%) Query: 209 GRGRPG-WHIECSAMSSHYLGKVFDI-HGGGLDLIFPH 244 G G P W + M H L ++DI H GL ++ P Sbjct: 254 GAGVPQDW---ATHMIGHELTALYDIDHAQGLAIVLPA 288 >gnl|CDD|37109 KOG1898, KOG1898, KOG1898, Splicing factor 3b, subunit 3 [RNA processing and modification]. Length = 1205 Score = 27.2 bits (60), Expect = 8.6 Identities = 10/40 (25%), Positives = 15/40 (37%) Query: 228 GKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIH 267 +VFD G + + +NE A S CA + Sbjct: 855 IRVFDPKSGKIICLVELGQNEAAFSVCAVDFSSSEYQPFV 894 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.320 0.136 0.415 Gapped Lambda K H 0.267 0.0692 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,833,313 Number of extensions: 314422 Number of successful extensions: 796 Number of sequences better than 10.0: 1 Number of HSP's gapped: 775 Number of HSP's successfully gapped: 44 Length of query: 461 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 364 Effective length of database: 4,167,664 Effective search space: 1517029696 Effective search space used: 1517029696 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 (21.8 bits) S2: 59 (26.6 bits)