RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781118|ref|YP_003065531.1| lysyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (502 letters) >gnl|CDD|179044 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed. Length = 491 Score = 724 bits (1871), Expect = 0.0 Identities = 238/485 (49%), Positives = 328/485 (67%), Gaps = 9/485 (1%) Query: 15 IEVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDE--KSQDMITVAGRVYSS 72 I VR +KL LR+ + YP F R T AE+R KY + +E + + ++VAGRV Sbjct: 7 IAVRREKLAELREQGIDPYPNKFERTHTAAELRAKYDDKEKEELEELEIEVSVAGRVMLK 66 Query: 73 RNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQVRRTKRGELTV 130 R G F + D SG+IQ++ KD +++ +D+GDIIG+ G + +TK GEL+V Sbjct: 67 RVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTGELSV 126 Query: 131 NAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFM 190 A ++ +L+K+L +P+ ++GL+DVE RYR+RY+D+I N +S+ F++RS +IS IR F+ Sbjct: 127 KATELTLLTKSLRPLPDKFHGLTDVETRYRQRYVDLIVNPESRETFRKRSKIISAIRRFL 186 Query: 191 EKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFE 250 + +GF+EVETP+LQPI GGA A PF THHN L D+YLRIAPELYLKR+++ G ++V+E Sbjct: 187 DNRGFLEVETPMLQPIAGGAAARPFITHHNALDIDLYLRIAPELYLKRLIVGGF-ERVYE 245 Query: 251 LNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEKV 310 + RNFRNEG+ +RHNPEFTM+E Y AY DY DMM L E+L +LA+ + GTT + + Sbjct: 246 IGRNFRNEGIDTRHNPEFTMLEFYQAYADYNDMMDLTEELIRHLAQAVLGTTKVTYQGTE 305 Query: 311 ISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEE 370 I F PF +M+ +KE TG+DF + + EAR A+ +GI VE G+++ +FEE Sbjct: 306 IDFGPPFKRLTMVDAIKEYTGVDFDDMTDE-EARALAKELGIEVEKSWGLGKLINELFEE 364 Query: 371 KIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRI 430 +E ++ PT ITD+P +ISP AK + L ERFE + G EI NAFSELNDP++QR Sbjct: 365 FVEPKLIQPTFITDYPVEISPLAKRHREDPGLTERFELFIGGREIANAFSELNDPIDQRE 424 Query: 431 RMEQQVEQSHQRG--EHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVIL 488 R E QVE G E +DEDFL A+ YGMPP GLG+GIDRL+MLLT++PSIRDVIL Sbjct: 425 RFEAQVEAKE-AGDDEAMFMDEDFLRALEYGMPPTGGLGIGIDRLVMLLTDSPSIRDVIL 483 Query: 489 FPAQR 493 FP R Sbjct: 484 FPLMR 488 >gnl|CDD|178118 PLN02502, PLN02502, lysyl-tRNA synthetase. Length = 553 Score = 544 bits (1405), Expect = e-155 Identities = 224/488 (45%), Positives = 308/488 (63%), Gaps = 14/488 (2%) Query: 16 EVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDEKSQD-MITVAGRVYSSRN 74 R +K+ LR E YP F T E++EKY L+N E+ +D ++VAGR+ + R Sbjct: 63 ANRLKKVEALRAKGVEPYPYKFDVTHTAPELQEKYGSLENGEELEDVSVSVAGRIMAKRA 122 Query: 75 SG--MFMDIHDASGKIQIFTHKDTADQDS---QNLLSMIDIGDIIGITGQVRRTKRGELT 129 G F D+ D GKIQ++ K D D + L S++D GDI+G+TG +TK+GEL+ Sbjct: 123 FGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELS 182 Query: 130 VNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHF 189 + +L+K L +P+ Y+GL+D E RYR+RYLD+I+N + + F+ R+ +IS IR F Sbjct: 183 IFPTSFEVLTKCLLMLPDKYHGLTDQETRYRQRYLDLIANPEVRDIFRTRAKIISYIRRF 242 Query: 190 MEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVF 249 ++ +GF+EVETP+L I GGA A PF THHN L D+YLRIA EL+LKR+++ G ++V+ Sbjct: 243 LDDRGFLEVETPMLNMIAGGAAARPFVTHHNDLNMDLYLRIATELHLKRLVVGGF-ERVY 301 Query: 250 ELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEK 309 E+ R FRNEG+S+RHNPEFT E Y AY DY DMM+L E++ + K L G+ I + Sbjct: 302 EIGRQFRNEGISTRHNPEFTTCEFYQAYADYNDMMELTEEMVSGMVKELTGSYKIKYHGI 361 Query: 310 VISFKAPFACKSMLQLVKEATGLDFMLLKSDQEAR----VAAQSIGITVENDALWGEVMM 365 I F PF SM+ LV+EATG+DF EA A + + G ++ Sbjct: 362 EIDFTPPFRRISMISLVEEATGIDFPADLKSDEANAYLIAACEKFDVKCPPPQTTGRLLN 421 Query: 366 TIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDP 425 +FEE +E+ +V PT + D P ++SP AK + L ERFE + NG E+ NAFSEL DP Sbjct: 422 ELFEEFLEETLVQPTFVLDHPVEMSPLAKPHRSKPGLTERFELFINGRELANAFSELTDP 481 Query: 426 VEQRIRMEQQVEQSHQRG--EHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSI 483 V+QR R E+QV+Q H G E LDEDF A+ YG+PP G GLGIDRL+MLLT++ SI Sbjct: 482 VDQRERFEEQVKQ-HNAGDDEAMALDEDFCTALEYGLPPTGGWGLGIDRLVMLLTDSASI 540 Query: 484 RDVILFPA 491 RDVI FPA Sbjct: 541 RDVIAFPA 548 >gnl|CDD|129590 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms. Length = 496 Score = 542 bits (1399), Expect = e-155 Identities = 232/493 (47%), Positives = 327/493 (66%), Gaps = 11/493 (2%) Query: 11 SSNSIEVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDE--KSQDMITVAGR 68 ++ ++ R +KL LR++ Y F R ++ E +E+Y+ L N+E +++AGR Sbjct: 2 LNDQLQTRREKLARLRQTGNNPYLNKFERTHSSQEFQEEYADLSNEELEDKNIEVSIAGR 61 Query: 69 VYSSRNSGM--FMDIHDASGKIQIFTHKDTADQDSQNL-LSMIDIGDIIGITGQVRRTKR 125 + + R+ G F+ + D SG+IQ++ +KD +D ++D+GDIIG+TG +TK Sbjct: 62 IMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKT 121 Query: 126 GELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQ 185 GEL+V+ ++ +L+KAL +P+ ++GL+D E RYR+RYLD+I N DS+ F RS +I Sbjct: 122 GELSVHVTELQILTKALRPLPDKFHGLTDQETRYRQRYLDLIVNPDSRQTFLVRSKIIKA 181 Query: 186 IRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLT 245 IR F++ +GF+EVETP+LQ I GGA A PF THHN L D+YLRIAPELYLKR+++ G Sbjct: 182 IRRFLDDRGFIEVETPMLQVIPGGANARPFITHHNALDMDLYLRIAPELYLKRLIVGGF- 240 Query: 246 DQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIP 305 ++V+E+ RNFRNEGV + HNPEFTMIE Y AY DY D+M L E+L LA+ L GTT I Sbjct: 241 EKVYEIGRNFRNEGVDTTHNPEFTMIEFYQAYADYEDLMDLTENLFKFLAQELLGTTKIT 300 Query: 306 FGEKVISFKAPFACKSMLQLVK---EATGLDFMLLKSDQEARVAAQSIGITVENDAL-WG 361 +GE I FK PF +M++ +K TG+DF LK + A+ A+ IGI V +L G Sbjct: 301 YGELEIDFKKPFKRITMVEAIKKYDMETGIDFDDLKDFETAKALAKKIGIEVAEKSLTLG 360 Query: 362 EVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSE 421 ++ +FE+ +E ++ PT IT +P +ISP AK +RFE + G EI NAFSE Sbjct: 361 HILNELFEQFLEHTLIQPTFITHYPAEISPLAKRNPSNPEFTDRFELFIAGKEIANAFSE 420 Query: 422 LNDPVEQRIRMEQQVEQSHQ-RGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNA 480 LNDP++QR R EQQV + E +DEDF++A+ YGMPP GLG+GIDRL+MLLT++ Sbjct: 421 LNDPLDQRERFEQQVAEKEAGDDEAQFVDEDFVEALEYGMPPTGGLGIGIDRLVMLLTDS 480 Query: 481 PSIRDVILFPAQR 493 SIRDVILFPA R Sbjct: 481 KSIRDVILFPAMR 493 >gnl|CDD|179519 PRK02983, lysS, lysyl-tRNA synthetase; Provisional. Length = 1094 Score = 425 bits (1096), Expect = e-119 Identities = 182/496 (36%), Positives = 267/496 (53%), Gaps = 39/496 (7%) Query: 17 VRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDEKSQDMITVAGRVYSSRNSG 76 VR KL LR + + YP T AE D + + ++V+GRV R+ G Sbjct: 616 VRLAKLEALRAAGVDPYPVGVPPTHTVAEAL--------DAPTGEEVSVSGRVLRIRDYG 667 Query: 77 --MFMDIHDASGKIQIFTHKDTADQDSQNL-LSMIDIGDIIGITGQVRRTKRGELTVNAQ 133 +F D+ D SG++Q+ +Q S + +D+GD++ +TG + ++ G L++ Sbjct: 668 GVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVT 727 Query: 134 KIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKK 193 + K L +P+ + GL+D E R R+RYLD+ N +++ + RS ++ +R + + Sbjct: 728 SWRLAGKCLRPLPDKWKGLTDPEARVRQRYLDLAVNPEARDLLRARSAVVRAVRETLVAR 787 Query: 194 GFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNR 253 GF+EVETPILQ ++GGA A PF TH N D+YLRIAPELYLKR+ + G+ ++VFEL R Sbjct: 788 GFLEVETPILQQVHGGANARPFVTHINAYDMDLYLRIAPELYLKRLCVGGV-ERVFELGR 846 Query: 254 NFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTT-----DIPFGE 308 NFRNEGV + HNPEFT++EAY A+ DY M L +L N A+ HG D Sbjct: 847 NFRNEGVDATHNPEFTLLEAYQAHADYDTMRDLTRELIQNAAQAAHGAPVVMRPDGDGVL 906 Query: 309 KVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMMTIF 368 + + P+ ++ V EA G + E R + GI D G V++ ++ Sbjct: 907 EPVDISGPWPVVTVHDAVSEALGEEIDPDTPLAELRKLCDAAGIPYRTDWDAGAVVLELY 966 Query: 369 EEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQ 428 E +E PT TDFP +SP + + L ER++ G E+ A+SEL DPVEQ Sbjct: 967 EHLVEDRTTFPTFYTDFPTSVSPLTRPHRSDPGLAERWDLVAWGVELGTAYSELTDPVEQ 1026 Query: 429 RIRMEQQ-----------VEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLL 477 R R+ +Q +E LDEDFL A+ Y MPP GLG+G+DRL+MLL Sbjct: 1027 RRRLTEQSLLAAGGDPEAME----------LDEDFLQALEYAMPPTGGLGMGVDRLVMLL 1076 Query: 478 TNAPSIRDVILFPAQR 493 T SIR+ + FP + Sbjct: 1077 TGR-SIRETLPFPLVK 1091 >gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed. Length = 505 Score = 412 bits (1059), Expect = e-115 Identities = 215/489 (43%), Positives = 318/489 (65%), Gaps = 9/489 (1%) Query: 12 SNSIEVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDE-KSQDM-ITVAGRV 69 ++ + R +KL LR+ +P F RD T+ ++ E++ N E +S ++ ++VAGR+ Sbjct: 16 NDELRNRREKLAALRQQ-GVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRM 74 Query: 70 YSSRNSGM--FMDIHDASGKIQIFTHKDTADQDSQN-LLSMIDIGDIIGITGQVRRTKRG 126 + R G F+ + D G+IQ++ +D+ + N D+GDIIG G + +T+ G Sbjct: 75 MTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTG 134 Query: 127 ELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQI 186 EL+++ ++ +L+KAL +P+ ++GL D E+RYR+RYLD+I+N S+ F RS +++ I Sbjct: 135 ELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAI 194 Query: 187 RHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTD 246 R FM +GFMEVETP++Q I GGA+A PF THHN L DMYLRIAPELYLKR+++ G + Sbjct: 195 RQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGF-E 253 Query: 247 QVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPF 306 +VFE+NRNFRNEG+S RHNPEFTM+E Y AY DY D+++L E L LA+ + GTT + + Sbjct: 254 RVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTY 313 Query: 307 GEKVISFKAPFACKSMLQLVKE-ATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMM 365 GE V F PF +M + +K+ D L + A+ A+SIGITVE G ++ Sbjct: 314 GEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVT 373 Query: 366 TIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDP 425 IF+E E +++ PT IT++P ++SP A+ + +RFE + G EI N FSELND Sbjct: 374 EIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDA 433 Query: 426 VEQRIRMEQQVE-QSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIR 484 +Q R ++QV ++ E DED++ A+ YG+PP +GLG+GIDR+IML TN+ +IR Sbjct: 434 EDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIR 493 Query: 485 DVILFPAQR 493 DVILFPA R Sbjct: 494 DVILFPAMR 502 >gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional. Length = 585 Score = 303 bits (777), Expect = 7e-83 Identities = 182/486 (37%), Positives = 262/486 (53%), Gaps = 26/486 (5%) Query: 33 YPAHFHRDITNAEVREKYSHLQNDEKSQDMI-TVAGRVYSSRNSGM---FMDIHDASGKI 88 YP F R IT E EKY L + E +D I V GR+ SG F D+ KI Sbjct: 104 YPHKFERTITVPEFVEKYQDLASGEHLEDTILNVTGRIMRVSASGQKLRFFDLVGDGAKI 163 Query: 89 QIFTHKDTADQDSQNLLSMIDI---GDIIGITGQVRRTKRGELTVNAQKIIMLSKALNSI 145 Q+ + D N D GDI+GI G ++K+GEL++ ++ I+LS L+ + Sbjct: 164 QVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETIILSPCLHML 223 Query: 146 PETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQP 205 P YGL D EIRYR+RYLD++ N ++ F R+ +I+ +R+F+ +GF+EVETP + Sbjct: 224 P-MKYGLKDTEIRYRQRYLDLMINESTRSTFITRTKIINYLRNFLNDRGFIEVETPTMNL 282 Query: 206 IYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHN 265 + GGA A PF THHN L D+YLRIA EL LK +++ G+ D+V+E+ + FRNEG+ + HN Sbjct: 283 VAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGI-DKVYEIGKVFRNEGIDNTHN 341 Query: 266 PEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEK-------VISFKAPFA 318 PEFT E YWAY D+ D++K ED L L GT I + + I F P+ Sbjct: 342 PEFTSCEFYWAYADFYDLIKWSEDFFSQLVMHLFGTYKILYNKDGPEKDPIEIDFTPPYP 401 Query: 319 CKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVE------NDALWGEVMMTIFEEKI 372 S+++ +++ T + L + + I + E N +++ + I Sbjct: 402 KVSIVEELEKLT--NTKLEQPFDSPETINKMINLIKENKIEMPNPPTAAKLLDQLASHFI 459 Query: 373 EKNIVN-PTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIR 431 E N P I + P+ +SP AK + L ER E + G E+ NA++ELNDP +Q+ Sbjct: 460 ENKYPNKPFFIIEHPQIMSPLAKYHRSKPGLTERLEMFICGKEVLNAYTELNDPFKQKEC 519 Query: 432 ME-QQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 QQ ++ E D F ++ YG+PP GLGLGIDR+ M LTN I+DVILFP Sbjct: 520 FSAQQKDREKGDAEAFQFDAAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNCIKDVILFP 579 Query: 491 AQRVKN 496 R N Sbjct: 580 TMRPAN 585 >gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional. Length = 659 Score = 288 bits (737), Expect = 3e-78 Identities = 167/482 (34%), Positives = 262/482 (54%), Gaps = 26/482 (5%) Query: 37 FHRDITNAEVREKYSHL-QNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTH 93 F +EVRE+Y +L D +Q + VAGRV S R+ G +F+ I ++Q+ Sbjct: 83 FRGITPISEVRERYGYLASGDRAAQATVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQ 142 Query: 94 --KDTADQDSQNLLSMIDIGDIIGITGQVRRTKRGELTVNAQKIIMLSKALNS----IPE 147 + +D + L + +GDIIG G R +RGEL+V A ++++LS + + P Sbjct: 143 VGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASRMLILSPYVCTDQVVCPN 202 Query: 148 T--YYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQP 205 + L D +++YR R+ D+++N ++R +++ +R + ++ F+EVETP+L Sbjct: 203 LRGFTVLQDNDVKYRYRFTDMMTNPCVIETIKKRHVMLQALRDYFNERNFVEVETPVLHT 262 Query: 206 IYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHN 265 + GA A F THHN D++LR+APEL+LK+ ++ G+ ++++E+ + FRNE HN Sbjct: 263 VASGANAKSFVTHHNANAMDLFLRVAPELHLKQCIVGGM-ERIYEIGKVFRNEDADRSHN 321 Query: 266 PEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPF-------GEKVISFKAPFA 318 PEFT E Y AY Y D+M + ED+ LA ++GTT + + PF Sbjct: 322 PEFTSCEFYAAYHTYEDLMPMTEDIFRQLAMRVNGTTVVQIYPENAHGNPVTVDLGKPFR 381 Query: 319 CKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMMT--IFEEKIE--- 373 S+ ++ +G++F + A + + + V +FE+ I+ Sbjct: 382 RVSVYDEIQRMSGVEFPPPNELNTPKGIAYMSVVMLRYNIPLPPVRTAAKMFEKLIDFFI 441 Query: 374 -KNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRM 432 +V PT + D P +SP AKE L ERFE + NG E CNA+SELNDP EQ R Sbjct: 442 TDRVVEPTFVMDHPLFMSPLAKEQVSRPGLAERFELFVNGIEYCNAYSELNDPHEQYHRF 501 Query: 433 EQQ-VEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFPA 491 +QQ V++ E LDE FL ++ G+PP +G G+GIDR +MLLTN+ +IRD I+FP Sbjct: 502 QQQLVDRQGGDEEAMPLDETFLKSLQVGLPPTAGWGMGIDRALMLLTNSSNIRDGIIFPL 561 Query: 492 QR 493 R Sbjct: 562 LR 563 >gnl|CDD|161889 TIGR00462, genX, lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown. Length = 304 Score = 253 bits (649), Expect = 6e-68 Identities = 109/322 (33%), Positives = 157/322 (48%), Gaps = 28/322 (8%) Query: 177 QQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATA---DPFKTH---HNILKADMYLRI 230 + R+ L++ IR F ++G +EVETP+L P T D F T + +YL+ Sbjct: 2 RARARLLAAIRAFFAERGVLEVETPLLSP--APVTDPHLDAFATEFLGPDGEGRPLYLQT 59 Query: 231 APELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDL 290 +PE +KR+L +G +F++ + FRN RHNPEFTM+E Y DY D+M VE L Sbjct: 60 SPEYAMKRLLAAGSGP-IFQICKVFRNGERGRRHNPEFTMLEWYRPGFDYHDLMDEVEAL 118 Query: 291 CHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSI 350 L AP+ S + G+D L S E AA + Sbjct: 119 LQELLGDP---------------FAPWERLSYQEAFLRYAGID-PLTASLDELAAAAAAH 162 Query: 351 GITVENDALWGEVMMTIFEEKIEKNIVN--PTHITDFPKDISPFAKEVAGEKRLVERFET 408 G+ + +++ +F EK+E ++ PT + D+P + A+ + R+ ERFE Sbjct: 163 GVRASEEDDRDDLLDLLFSEKVEPHLGFGRPTFLYDYPASQAALARISPDDPRVAERFEL 222 Query: 409 YCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTI-LDEDFLDAMTYGMPPASGLG 467 Y G E+ N F EL D EQR R E + G LDE FL A+ G+P SG+ Sbjct: 223 YIKGLELANGFHELTDAAEQRRRFEADNAERKALGLPRYPLDERFLAALEAGLPECSGVA 282 Query: 468 LGIDRLIMLLTNAPSIRDVILF 489 LG+DRL+ML A SI DV+ F Sbjct: 283 LGVDRLLMLALGADSIDDVLAF 304 >gnl|CDD|181791 PRK09350, PRK09350, poxB regulator PoxA; Provisional. Length = 306 Score = 200 bits (510), Expect = 9e-52 Identities = 106/336 (31%), Positives = 156/336 (46%), Gaps = 51/336 (15%) Query: 172 SKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATA-----DPFKTH----HNIL 222 S +R+ +I++IR F +G +EVETPIL AT PF+T Sbjct: 1 SIPNLLKRAKIIAEIRRFFADRGVLEVETPILSQ----ATVTDIHLVPFETRFVGPGASQ 56 Query: 223 KADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRD 282 ++L +PE ++KR+L +G +F++ ++FRNE HNPEFTM+E Y + D Sbjct: 57 GKTLWLMTSPEYHMKRLLAAGSGP-IFQICKSFRNEEAGRYHNPEFTMLEWYRPHYDMYR 115 Query: 283 MMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPF--------ACKSMLQLVKEATGLDF 334 +M V+DL + + +S++ F QL + A L Sbjct: 116 LMNEVDDLLQQVLDCEPA--------ESLSYQQAFLRYLGIDPLSADKTQLREVAAKLGL 167 Query: 335 MLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEEKIEKNIVN--PTHITDFPKDISPF 392 + ++E R D L + +F +E NI PT + FP + Sbjct: 168 SNIADEEEDR------------DTL----LQLLFTFGVEPNIGKEKPTFVYHFPASQAAL 211 Query: 393 AKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRG--EHTILDE 450 AK + R+ ERFE Y G E+ N F EL D EQR R EQ + RG + I DE Sbjct: 212 AKISTEDHRVAERFEVYFKGIELANGFHELTDAREQRQRFEQDNRKRAARGLPQQPI-DE 270 Query: 451 DFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDV 486 + + A+ G+P SG+ LG+DRLIML A SI +V Sbjct: 271 NLIAALEAGLPDCSGVALGVDRLIMLALGAESISEV 306 >gnl|CDD|129550 TIGR00458, aspS_arch, aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). Length = 428 Score = 130 bits (328), Expect = 8e-31 Identities = 114/452 (25%), Positives = 204/452 (45%), Gaps = 52/452 (11%) Query: 57 EKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDII 114 E +T G V+ R+ G +F+ + D G IQI ++ +++ ++ Sbjct: 9 EMDGQEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVV 68 Query: 115 GITGQVRRTKR--GELTVNAQKIIMLSKALNSIPETYYGLSDVEI--RYRKRYLDIISNS 170 + G V+ ++ G + KI ++++A +P E+ R R+LD+ + Sbjct: 69 AVRGIVKIKEKAPGGFEIIPTKIEVINEAKEPLPLDPTEKVPAELDTRLDYRFLDLRRPT 128 Query: 171 DSKIRFQQRSLLISQIRHFMEKKGFMEVETPIL--QPIYGGATADPFKTHHNILKADMYL 228 I F+ RS ++ +R F+ ++GF+EV TP L GG P + + +L Sbjct: 129 VQAI-FRIRSGVLESVREFLAEEGFIEVHTPKLVASATEGGTELFPI----TYFEREAFL 183 Query: 229 RIAPELYLKRVLISGLTDQVFELNRNFRNEGVSS-RHNPEFTMIEAYWAYTDYRDMMKLV 287 +P+LY K+ L++ ++V+E+ FR E ++ RH E T I+ A+ D+ D+M ++ Sbjct: 184 GQSPQLY-KQQLMAAGFERVYEIGPIFRAEEHNTHRHLNEATSIDIEMAFEDHHDVMDIL 242 Query: 288 EDLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAA 347 E+L + + + + P F+ L D EA A Sbjct: 243 EELVVRVFEDVPERCAHQLETLEFKLEKP--------------EGKFVRLTYD-EAIEMA 287 Query: 348 QSIGITVENDALWGEVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFE 407 + G+ + WGE + T E+ + + + ITD+P +I PF + E Sbjct: 288 NAKGVEIG----WGEDLSTEAEKALGEEMDGLYFITDWPTEIRPFYT-MPDEDNP----- 337 Query: 408 TYCNGWEICNAFSELNDPVE-----QRIRM-EQQVEQSHQRGEHTILDEDFLDAMTYGMP 461 EI +F + +E QRI + + VE+ +G + +D+L+A +YGMP Sbjct: 338 ------EISKSFDLMYRDLEISSGAQRIHLHDLLVERIKAKGLNPEGFKDYLEAFSYGMP 391 Query: 462 PASGLGLGIDRLIMLLTNAPSIRDVILFPAQR 493 P +G GLG +R +M L +IR+ +LFP R Sbjct: 392 PHAGWGLGAERFVMFLLGLKNIREAVLFPRDR 423 >gnl|CDD|179948 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional. Length = 437 Score = 127 bits (321), Expect = 7e-30 Identities = 120/459 (26%), Positives = 205/459 (44%), Gaps = 79/459 (17%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 +T+AG V+ R+ G F+ + D SG IQ+ K D++ + + ++ +TG V Sbjct: 19 VTLAGWVHEIRDLGGIAFLILRDRSGIIQV-VVKKKVDEELFETIKKLKRESVVSVTGTV 77 Query: 121 R---RTKRG-ELTVNAQKIIMLSKALNSIPETYYGLSDVEI--RYRKRYLDIISNSDSKI 174 + + G E+ ++I +L+KA +P G E+ R R+LD+ + Sbjct: 78 KANPKAPGGVEVIP--EEIEVLNKAEEPLPLDISGKVLAELDTRLDNRFLDL-RRPRVRA 134 Query: 175 RFQQRSLLISQIRHFMEKKGFMEVETP--ILQPIYGGATADPFKTHHNILKADMYLRIAP 232 F+ RS ++ R F+ + GF E+ TP + GGA P + YL +P Sbjct: 135 IFKIRSEVLRAFREFLYENGFTEIFTPKIVASGTEGGAELFPIDYFEK----EAYLAQSP 190 Query: 233 ELYLKRVLISGLTDQVFELNRNFRNE-GVSSRHNPEFTMIEAYWAYTD-YRDMMKLVEDL 290 +LY K++++ ++VFE+ FR E +SRH E+T I+ + D + D+M L+E+L Sbjct: 191 QLY-KQMMVGAGFERVFEIGPVFRAEEHNTSRHLNEYTSIDVEMGFIDDHEDVMDLLENL 249 Query: 291 CHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSD------QEAR 344 + + + C+ L+L+ G++ + ++ EA Sbjct: 250 LRYMYEDVAEN-----------------CEKELELL----GIELPVPETPIPRITYDEAI 288 Query: 345 VAAQSIGITVENDALWGEVMMTIFEEKIEKNIVNPTH------ITDFPKDISPF-AKEVA 397 +S G + WG+ + T E++ V + ITD+P + PF Sbjct: 289 EILKSKGNEIS----WGDDLDT-EGERLLGEYVKEEYGSDFYFITDYPSEKRPFYTMP-- 341 Query: 398 GEKRLVERFETYCNGWEICNAFSELNDPVE-----QRI-RMEQQVEQSHQRGEHTILDED 451 + EI +F L +E QRI R + VE ++G + E Sbjct: 342 -----------DEDDPEISKSFDLLFRGLEITSGGQRIHRYDMLVESIKEKGLNPESFEF 390 Query: 452 FLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 +L+A YGMPP G GLG++RL M L +IR+ +LFP Sbjct: 391 YLEAFKYGMPPHGGFGLGLERLTMKLLGLENIREAVLFP 429 >gnl|CDD|161887 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn. Length = 453 Score = 114 bits (288), Expect = 4e-26 Identities = 107/464 (23%), Positives = 190/464 (40%), Gaps = 63/464 (13%) Query: 58 KSQDMITVAGRVYSSRNSG--MFMDIHDAS--GKIQIFTHKDTADQDSQNLLSMIDIGDI 113 D +TV+G V + R+S +F++++D S G IQ + + Q L S + G Sbjct: 14 FVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKS-LTTGSS 72 Query: 114 IGITGQVRRT--KRGELTVNAQKIIMLSKALNSIPETY----------YGLSDVEIRYRK 161 + +TG+V + K + + +KI ++ +A P+ Y + +R R Sbjct: 73 VSVTGKVVESPGKGQPVELQVKKIEVVGEA---EPDDYPLQKKEHSLEFLRDIAHLRLRT 129 Query: 162 RYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKT-HHN 220 L + ++R + L I + ++ GF V PIL + F+ Sbjct: 130 NTLGAVM----RVR----NALSQAIHRYFQENGFTWVSPPILTSNDCEGAGELFRVSTDG 181 Query: 221 ILKA------DMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGV-SSRHNPEFTMIEA 273 I + + YL ++ +LYL+ ++ +V+ FR E +SRH EF MIE Sbjct: 182 IDFSQDFFGKEAYLTVSGQLYLETYALA--LSKVYTFGPTFRAEKSNTSRHLSEFWMIEP 239 Query: 274 YWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLD 333 A+ + D+++L E L + K + +F + ++ Sbjct: 240 EMAFANLNDLLQLAETLIKYIIKAVLENCSQELKFLEKNFDKDLIKR-----LENIINNK 294 Query: 334 FMLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEEKI-EKNIVNPTHITDFPKDISPF 392 F + + +S E + WG+ + T E + E+ P +T++PKDI F Sbjct: 295 FARITYTDAIEILKES-DKNFEYEDFWGDDLQTEHERFLAEEYFKPPVFVTNYPKDIKAF 353 Query: 393 AKEVAGEKRLVERFETYCNGW-EICNAFSELNDPVEQRI-RMEQQVEQSHQRGEHTILDE 450 ++ + + V + G EI +R +++ + + G LD Sbjct: 354 YMKLNDDGKTVAAMDLLAPGIGEIIGG--------SEREDDLDKLENRMKEMG----LDT 401 Query: 451 D----FLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 D +LD YG P SG GLG +RL+ +T +IRD I FP Sbjct: 402 DALNWYLDLRKYGSVPHSGFGLGFERLLAYITGLENIRDAIPFP 445 >gnl|CDD|179678 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated. Length = 450 Score = 95.9 bits (240), Expect = 2e-20 Identities = 118/478 (24%), Positives = 184/478 (38%), Gaps = 104/478 (21%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 +TV G V + R+SG F+ + D S Q+ KD ++ + + G + +TG V Sbjct: 19 VTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKD-NGEEYFEEIKKLTTGSSVIVTGTV 77 Query: 121 RRTKR--GELTVNAQKIIMLSKALNSIPETY----------YGLSDVEIRYRKRYLDIIS 168 + R + A KI ++ + PE Y + L ++ +L + Sbjct: 78 VESPRAGQGYELQATKIEVIGED----PEDYPIQKKRHSIEF-LREI------AHLRPRT 126 Query: 169 NSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADM-- 226 N + + R+ L I F + GF+ V+TPI+ + F+ L Sbjct: 127 NKFGAV-MRIRNTLAQAIHEFFNENGFVWVDTPIITASDCEGAGELFRVTTLDLDFSKDF 185 Query: 227 -----YLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVS--SRHNPEFTMIEAYWAYTD 279 YL ++ +LY + L V+ FR E S RH EF MIE A+ D Sbjct: 186 FGKEAYLTVSGQLYAE-AYAMALGK-VYTFGPTFRAEN-SNTRRHLAEFWMIEPEMAFAD 242 Query: 280 YRDMMKLVED-LCHNLAKTL-HGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLL 337 D M L E+ L + + L + D+ F + + K ++ ++ F + Sbjct: 243 LEDNMDLAEEMLKYVVKYVLENCPDDLEFLNRRVD-------KGDIERLENFIESPFPRI 295 Query: 338 KSDQEARVAAQSIGITVENDALWGEVMMT-----IFEEKIEKNIVNPTHITDFPKDISPF 392 EA Q G E WG+ + + + EE +K P +T++PKDI F Sbjct: 296 TYT-EAIEILQKSGKKFEFPVEWGDDLGSEHERYLAEEHFKK----PVFVTNYPKDIKAF 350 Query: 393 -------AKEVAGEKRLV----------ERFETYCNGWEICNAFSELNDPVEQRIRMEQQ 435 K VA L +R E D +E RI+ Sbjct: 351 YMRLNPDGKTVAAMDLLAPGIGEIIGGSQREERL--------------DVLEARIK---- 392 Query: 436 VEQSHQRGEHTILDEDF---LDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 E + ED+ LD YG P SG GLG +RL+ +T +IRDVI FP Sbjct: 393 --------ELGLNKEDYWWYLDLRRYGSVPHSGFGLGFERLVAYITGLDNIRDVIPFP 442 >gnl|CDD|129551 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences. Length = 583 Score = 96.0 bits (239), Expect = 2e-20 Identities = 70/264 (26%), Positives = 134/264 (50%), Gaps = 33/264 (12%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 +T+AG V R+ G +F+D+ D SG +Q+ D D+ L + D++ + G+V Sbjct: 18 VTLAGWVNRRRDLGGLIFIDLRDRSGIVQVV---CDPDADALKLAKGLRNEDVVQVKGKV 74 Query: 121 ---------RRTKRGELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSD 171 R GE+ + A+ I +L+K+ ++ E+R + RYLD+ + Sbjct: 75 SARPEGNINRNLDTGEIEILAESITLLNKSKTPPLIIEKTDAEEEVRLKYRYLDL-RRPE 133 Query: 172 SKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATAD-------PFKTHHNILKA 224 + R + R + +R+F++++GF+E+ETP+L +T + P + H K Sbjct: 134 MQQRLKLRHKVTKAVRNFLDQQGFLEIETPMLT----KSTPEGARDYLVPSRVH----KG 185 Query: 225 DMY-LRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDM 283 + Y L +P+L+ K++L+ D+ +++ R FR+E + + PEFT I+ ++ D+ Sbjct: 186 EFYALPQSPQLF-KQLLMVSGVDRYYQIARCFRDEDLRADRQPEFTQIDMEMSFMTQEDV 244 Query: 284 MKLVEDLCHNLAKTLHGTT-DIPF 306 M+L+E L ++ + G PF Sbjct: 245 MELIEKLVSHVFLEVKGIDLKKPF 268 Score = 74.0 bits (182), Expect = 8e-14 Identities = 43/124 (34%), Positives = 63/124 (50%), Gaps = 5/124 (4%) Query: 368 FEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDP-V 426 FE+ E + H PKD E A E+ L E ++ NG E+ ++DP V Sbjct: 432 FEKDKEGRLCAAHHPFTMPKDEDLENLEAAPEEALAEAYDLVLNGVELGGGSIRIHDPEV 491 Query: 427 EQRIRMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDV 486 ++++ ++ R + L L+A YG PP +G LG+DRL+MLLT +IRDV Sbjct: 492 QKKVFEILGIDPEEAREKFGFL----LEAFKYGTPPHAGFALGLDRLMMLLTGTDNIRDV 547 Query: 487 ILFP 490 I FP Sbjct: 548 IAFP 551 >gnl|CDD|178491 PLN02903, PLN02903, aminoacyl-tRNA ligase. Length = 652 Score = 81.8 bits (202), Expect = 4e-16 Identities = 67/251 (26%), Positives = 123/251 (49%), Gaps = 27/251 (10%) Query: 61 DMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITG 118 +T+ G V R+ G F+D+ D +G +Q+ T D ++ + + ++ + G Sbjct: 73 SRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEF-PEAHRTANRLRNEYVVAVEG 131 Query: 119 QVR---------RTKRGELTVNAQKIIMLSKALNSIPETYYGLSDV------EIRYRKRY 163 VR + K G + V A+ + +L+ S+P + E+R R R Sbjct: 132 TVRSRPQESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVTTADEQKDSIKEEVRLRYRV 191 Query: 164 LDI-ISNSDSKIRFQQRSLLISQIRHFME-KKGFMEVETPIL-QPIYGGATADPFKTHHN 220 LD+ ++ +R + R ++ IR ++E GF+E+ETPIL + GA + Sbjct: 192 LDLRRPQMNANLRLRHR--VVKLIRRYLEDVHGFVEIETPILSRSTPEGARDYLVPSR-- 247 Query: 221 ILKADMY-LRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTD 279 + Y L +P+L+ + +++SG D+ +++ R FR+E + + PEFT ++ A+T Sbjct: 248 VQPGTFYALPQSPQLFKQMLMVSGF-DRYYQIARCFRDEDLRADRQPEFTQLDMELAFTP 306 Query: 280 YRDMMKLVEDL 290 DM+KL EDL Sbjct: 307 LEDMLKLNEDL 317 Score = 61.7 bits (150), Expect = 4e-10 Identities = 22/38 (57%), Positives = 27/38 (71%) Query: 453 LDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 L+A+ G PP G+ G+DRL+MLL A SIRDVI FP Sbjct: 582 LEALDMGAPPHGGIAYGLDRLVMLLAGAKSIRDVIAFP 619 >gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional. Length = 550 Score = 77.3 bits (190), Expect = 7e-15 Identities = 113/497 (22%), Positives = 209/497 (42%), Gaps = 74/497 (14%) Query: 53 LQNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTH------KDTADQDSQ-N 103 L E + + RV ++R G FM + D S +Q K+ D Q Sbjct: 71 LSKPELVDKTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIP 130 Query: 104 LLSMIDIGDIIGITGQ-VRRTKRGELTVNAQKIIMLSKALNSIPETYYGLS--------- 153 S++D+ + Q + T ++ + +KI ++++L ++P T S Sbjct: 131 TESIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTESLRTLPFTLEDASRKESDEGAK 190 Query: 154 -DVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETP--ILQPIYGGA 210 + + R R++D+ + + I F+ +S + R F+ F E+ +P I P GGA Sbjct: 191 VNFDTRLNSRWMDLRTPASGAI-FRLQSRVCQYFRQFLIDSDFCEIHSPKIINAPSEGGA 249 Query: 211 TADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSS-RHNPEFT 269 FK + YL +P+LY K++++ G +VFE+ FR+E ++ RH EF Sbjct: 250 NV--FKLEY--FNRFAYLAQSPQLY-KQMVLQGDVPRVFEVGPVFRSENSNTHRHLTEFV 304 Query: 270 MIEAYWAYTD-YRDMMKLVEDL-CHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVK 327 ++ + Y +++ L E L + + T ++ + F+ P K + +K Sbjct: 305 GLDVEMRINEHYYEVLDLAESLFNYIFERLATHTKELKAVCQQYPFE-PLVWKLTPERMK 363 Query: 328 EATGLDFMLLKSDQE------ARVAAQSIGITVENDALWGEVMMTIFEEKIE-KNIVNPT 380 E L ++ E ARV + N E++ T+ EEK+ + +N T Sbjct: 364 E---LGVGVISEGVEPTDKYQARVHNMDSRMLRINYMHCIELLNTVLEEKMAPTDDINTT 420 Query: 381 H-----------------ITD-FPKDISPF-AKEVAGEKRLVERFETYCNGWEICNAFSE 421 + I+D FP PF E ++R ++ + G EI + Sbjct: 421 NEKLLGKLVKERYGTDFFISDRFPSSARPFYTMECKDDERFTNSYDMFIRGEEISSGAQR 480 Query: 422 LNDP--VEQRIRMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTN 479 ++DP + R +M V+ + + +++D+ G P G G+G++R++ML Sbjct: 481 IHDPDLLLARAKM-LNVDLTPIK--------EYVDSFRLGAWPHGGFGVGLERVVMLYLG 531 Query: 480 APSIRDVILFP--AQRV 494 ++R LFP QR Sbjct: 532 LSNVRLASLFPRDPQRT 548 >gnl|CDD|179042 PRK00476, aspS, aspartyl-tRNA synthetase; Validated. Length = 588 Score = 76.6 bits (190), Expect = 1e-14 Identities = 56/185 (30%), Positives = 90/185 (48%), Gaps = 34/185 (18%) Query: 36 HFHRDITNAEVREKYSHLQNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTH 93 H R E+RE SH+ + +T+ G V+ R+ G +F+D+ D G +Q+ Sbjct: 1 HMMRTHYCGELRE--SHV--GQT----VTLCGWVHRRRDHGGLIFIDLRDREGIVQV--- 49 Query: 94 KDTADQDSQNLLSMIDIG--DIIGITGQVRRTKRGELTVN-----------AQKIIMLSK 140 D D++ + +I +TG VR R E TVN A ++ +L+K Sbjct: 50 --VFDPDAEAFEVAESLRSEYVIQVTGTVR--ARPEGTVNPNLPTGEIEVLASELEVLNK 105 Query: 141 ALNSIPETYYGLSDV--EIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEV 198 + ++P DV E+R + RYLD+ K + RS + S IR+F++ GF+E+ Sbjct: 106 S-KTLPFPIDDEEDVSEELRLKYRYLDLRRPEMQK-NLKLRSKVTSAIRNFLDDNGFLEI 163 Query: 199 ETPIL 203 ETPIL Sbjct: 164 ETPIL 168 Score = 74.7 bits (185), Expect = 4e-14 Identities = 26/47 (55%), Positives = 30/47 (63%), Gaps = 4/47 (8%) Query: 452 FLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFPAQRVKNGS 498 LDA+ YG PP G+ G+DRL+MLL A SIRDVI FP K S Sbjct: 518 LLDALKYGAPPHGGIAFGLDRLVMLLAGADSIRDVIAFP----KTQS 560 >gnl|CDD|180575 PRK06462, PRK06462, asparagine synthetase A; Reviewed. Length = 335 Score = 74.3 bits (183), Expect = 6e-14 Identities = 90/369 (24%), Positives = 141/369 (38%), Gaps = 78/369 (21%) Query: 156 EIRYRKRYLDIISNSDSKIR-------FQQRSLLISQIRHFMEKKGFMEVETPILQPI-- 206 RY K Y + + S I + +S ++ R F++ +GF+EV PI+ P Sbjct: 3 LERYPKEYEEFLRMSWKHISSEKYRKVLKVQSSILRYTREFLDGRGFVEVLPPIISPSTD 62 Query: 207 --YGGATADPFKTHH-NILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSS- 262 G + P K + + YL + L+ K++ + L ++F L+ NFR E V Sbjct: 63 PLMGLGSDLPVKQISIDFYGVEYYLADSMILH-KQLALRML-GKIFYLSPNFRLEPVDKD 120 Query: 263 --RHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTL---HGTTDIPFGEKVISFKAPF 317 RH EFT ++ D ++M L+EDL L K L H FG + K PF Sbjct: 121 TGRHLYEFTQLDIEIEGADLDEVMDLIEDLIKYLVKELLEEHEDELEFFGRDLPHLKRPF 180 Query: 318 -------ACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEE 370 A + + + G+D L S+ E + FEE Sbjct: 181 KRITHKEAVEILNEEGCR--GIDLEELGSEGEK-------------------SLSEHFEE 219 Query: 371 KIEKNIVNPTHITDFPKDISPF----AKEVAGEKR-----LVERFETYCNGWEICNAFSE 421 P I D PK F E G R L E + +G E + E Sbjct: 220 --------PFWIIDIPKGSREFYDREDPERPGVLRNYDLLLPEGYGEAVSGGEREYEYEE 271 Query: 422 LNDPVEQRIRMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAP 481 + +RIR + ++ +L+ G P++G G+G++RL + Sbjct: 272 ----IVERIREHGVDPEKYK---------WYLEMAKEGPLPSAGFGIGVERLTRYICGLR 318 Query: 482 SIRDVILFP 490 IR+V FP Sbjct: 319 HIREVQPFP 327 >gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional. Length = 706 Score = 68.5 bits (167), Expect = 4e-12 Identities = 64/256 (25%), Positives = 119/256 (46%), Gaps = 35/256 (13%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 + +AG V + R+ G +F+ + D +G IQ + A D L + + + + G+V Sbjct: 21 VCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEV 80 Query: 121 RRTKRGELTVNAQ----KIIMLSKALNSIPETY---YGLSDV----------------EI 157 ++ R E T N I + + L+ + + + +SD ++ Sbjct: 81 QK--RLEETENPHIETGDIEVFVRELSILAASEALPFAISDKAMTAGAGSAGADAVNEDL 138 Query: 158 RYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATAD---P 214 R + RYLDI + +R +I R F++ +GF+E+ETPIL D P Sbjct: 139 RLQYRYLDIRRPAMQD-HLAKRHRIIKCARDFLDSRGFLEIETPILTKSTPEGARDYLVP 197 Query: 215 FKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAY 274 + H A L +P+L+ + ++I+G ++ F+L R FR+E + PEFT ++ Sbjct: 198 SRIHPKEFYA---LPQSPQLFKQLLMIAGF-ERYFQLARCFRDEDLRPNRQPEFTQLDIE 253 Query: 275 WAYTDYRDMMKLVEDL 290 ++ D + +L+E+L Sbjct: 254 ASFIDEEFIFELIEEL 269 Score = 51.1 bits (122), Expect = 6e-07 Identities = 19/42 (45%), Positives = 27/42 (64%) Query: 452 FLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFPAQR 493 FL A + PP G+ LG+DR++ ++ PSIR+VI FP R Sbjct: 534 FLRAFDFAAPPHGGIALGLDRVVSMILQTPSIREVIAFPKNR 575 >gnl|CDD|178442 PLN02850, PLN02850, aspartate-tRNA ligase. Length = 530 Score = 63.6 bits (155), Expect = 1e-10 Identities = 90/363 (24%), Positives = 156/363 (42%), Gaps = 74/363 (20%) Query: 156 EIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGAT---A 212 + R R LD+ + ++ I F+ +S + + R F+ KGF+E+ TP L GA+ + Sbjct: 206 DTRLNNRVLDLRTPANQAI-FRIQSQVCNLFREFLLSKGFVEIHTPKL---IAGASEGGS 261 Query: 213 DPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNE-GVSSRHNPEFTMI 271 F+ + A L +P+L+ K++ I G +VFE+ FR E + RH EFT + Sbjct: 262 AVFRLDYKGQPA--CLAQSPQLH-KQMAICGDFRRVFEIGPVFRAEDSFTHRHLCEFTGL 318 Query: 272 EAYWAYTD-YRDMMKLVEDLC--------HNLAKTLHGTTDIPFGEKVISFKAPFACKSM 322 + + Y +++ +V++L K L + I + PF Sbjct: 319 DLEMEIKEHYSEVLDVVDELFVAIFDGLNERCKKEL----------EAIREQYPF---EP 365 Query: 323 LQLVKEATGLDF-----MLLKSDQEARVAAQSIG-ITVENDALWGEVMMTIFEEKIEKNI 376 L+ + + L F ML +EA V +G + E+ E+ + Sbjct: 366 LKYLPKTLRLTFAEGIQML----KEAGVEVDPLGDLNTES-------------ERKLGQL 408 Query: 377 VNPTHITDF------PKDISPF-AKEVAGEKRLVERFETYCNGWEICNAFSELNDP--VE 427 V + TDF P + PF + + F+ + G EI + ++DP +E Sbjct: 409 VKEKYGTDFYILHRYPLAVRPFYTMPCPDDPKYSNSFDVFIRGEEIISGAQRVHDPELLE 468 Query: 428 QRIRMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVI 487 +R E ++ TI ++D+ YG PP G G+G++R++ML +IR Sbjct: 469 KRAE-ECGIDVK------TI--STYIDSFRYGAPPHGGFGVGLERVVMLFCGLNNIRKTS 519 Query: 488 LFP 490 LFP Sbjct: 520 LFP 522 >gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase. Length = 565 Score = 59.2 bits (143), Expect = 2e-09 Identities = 74/270 (27%), Positives = 108/270 (40%), Gaps = 52/270 (19%) Query: 242 SGLTDQVFELNRNFRNEGV-SSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTL-- 298 + L+D V+ FR E +SRH EF MIE A+ D D M + K + Sbjct: 319 TALSD-VYTFGPTFRAENSNTSRHLAEFWMIEPELAFADLNDDMACATAYLQYVVKYILE 377 Query: 299 HGTTDIPFG----EK-VISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGIT 353 + D+ F EK +I + K+ +QL T +LLK+ ++ Sbjct: 378 NCKEDMEFFNTWIEKGIIDRLSDVVEKNFVQL--SYTDAIELLLKAKKK----------- 424 Query: 354 VENDALWGEVMMTIFEEKIEKNIVN--PTHITDFPKDISPF-------AKEVAGEKRLVE 404 E WG + + E I + P I D+PK+I F K VA LV Sbjct: 425 FEFPVKWGLDLQSEHERYITEEAFGGRPVIIRDYPKEIKAFYMRENDDGKTVAAMDMLVP 484 Query: 405 RFETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTILDED----FLDAMTYGM 460 R G QR E+++E R + L+++ +LD YG Sbjct: 485 RVGELIGG--------------SQR---EERLEYLEARLDELKLNKESYWWYLDLRRYGS 527 Query: 461 PPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 P +G GLG +RL+ T +IRD I FP Sbjct: 528 VPHAGFGLGFERLVQFATGIDNIRDAIPFP 557 >gnl|CDD|178147 PLN02532, PLN02532, asparagine-tRNA synthetase. Length = 633 Score = 58.3 bits (141), Expect = 4e-09 Identities = 57/258 (22%), Positives = 103/258 (39%), Gaps = 29/258 (11%) Query: 248 VFELNRNFRNEG-VSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTL--HGTTDI 304 V+ FR + S+RH E M+E A+++ D M ED L K + + + D+ Sbjct: 392 VYTFGPRFRADRIDSARHLAEMWMVEVEMAFSELEDAMNCAEDYFKFLCKWVLENCSEDM 451 Query: 305 PFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALWG--- 361 F K I K++ ++ + + + Q+ E WG Sbjct: 452 KFVSKRID-------KTISTRLEAIISSSLQRISYTEAVDLLKQATDKKFETKPEWGIAL 504 Query: 362 -EVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYC--NGWEICNA 418 ++ ++I K P I ++PK++ PF + + + V F+ G I + Sbjct: 505 TTEHLSYLADEIYKK---PVIIYNYPKELKPFYVRLNDDGKTVAAFDLVVPKVGTVITGS 561 Query: 419 FSELNDPVEQRIRM-EQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLL 477 +E +R+ + ++E+ E E +LD +G SG LG + +++ Sbjct: 562 QNE------ERMDILNARIEELGLPREQY---EWYLDLRRHGTVKHSGFSLGFELMVLFA 612 Query: 478 TNAPSIRDVILFPAQRVK 495 T P +RD I FP K Sbjct: 613 TGLPDVRDAIPFPRSWGK 630 >gnl|CDD|185610 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional. Length = 586 Score = 55.8 bits (134), Expect = 3e-08 Identities = 72/285 (25%), Positives = 114/285 (40%), Gaps = 54/285 (18%) Query: 227 YLRIAPELYLKRVLISGLTDQVFELNRNFRNEGV-SSRHNPEFTMIEAYWAYTDYRDMMK 285 +L ++ +L L+ L S + D V+ FR E +SRH EF MIE A+ D D M+ Sbjct: 327 FLTVSGQLSLEN-LCSSMGD-VYTFGPTFRAENSHTSRHLAEFWMIEPEIAFADLYDNME 384 Query: 286 LVED-----LCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQ----LVKEATGLDFML 336 L E + + L DI + E+ + K++L + +D + Sbjct: 385 LAESYIKYCIGYVLNNNFD---DIYYFEENVETGLISRLKNILDEDFAKITYTNVIDLLQ 441 Query: 337 LKSDQEARVAAQSIGITVENDALWGEVMMTIFEEKIEKNIVN-PTHITDFPKDISPF--- 392 SD E WG + + E + + I P + ++PKD+ F Sbjct: 442 PYSDS------------FEVPVKWGMDLQSEHERFVAEQIFKKPVIVYNYPKDLKAFYMK 489 Query: 393 ----AKEVAGEKRLVERFETYCNGWEICNAFSELNDPV-EQRIRMEQQ--VEQSHQRGEH 445 K VA LV + G + + L+ + E+++ ME Q + G H Sbjct: 490 LNEDQKTVAAMDVLVPKIGEVIGGSQREDNLERLDKMIKEKKLNMESYWWYRQLRKFGSH 549 Query: 446 TILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 P +G GLG +RLIML+T +I+D I FP Sbjct: 550 ----------------PHAGFGLGFERLIMLVTGVDNIKDTIPFP 578 >gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase. Length = 572 Score = 52.7 bits (126), Expect = 2e-07 Identities = 66/257 (25%), Positives = 100/257 (38%), Gaps = 35/257 (13%) Query: 248 VFELNRNFRNEGV-SSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGT--TDI 304 V+ FR E +SRH EF M+E A+ D D M E + K L D+ Sbjct: 329 VYTFGPTFRAENSHTSRHLAEFWMVEPEIAFADLEDDMNCAEAYVKYMCKWLLDKCFDDM 388 Query: 305 PFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSI--GITVENDALWGE 362 K C L++V F + + + +++ G +N+ WG Sbjct: 389 ELMAKNFDS----GCIDRLRMVASTP---FGRITYTEAIELLEEAVAKGKEFDNNVEWGI 441 Query: 363 VMMTIFEEKIEKNIVN-PTHITDFPKDISPF-------AKEVAGEKRLVERFETYCNGWE 414 + + E + + + P + ++PK I F K VA LV + G Sbjct: 442 DLASEHERYLTEVLFQKPLIVYNYPKGIKAFYMRLNDDEKTVAAMDVLVPKVGELIGG-- 499 Query: 415 ICNAFSELNDPVEQRI-RMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRL 473 + E D ++QRI M +E E +LD YG G GLG +R+ Sbjct: 500 --SQREERYDVIKQRIEEMGLPIEPY----------EWYLDLRRYGTVKHCGFGLGFERM 547 Query: 474 IMLLTNAPSIRDVILFP 490 I+ T +IRDVI FP Sbjct: 548 ILFATGIDNIRDVIPFP 564 >gnl|CDD|181936 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed. Length = 417 Score = 39.8 bits (93), Expect = 0.001 Identities = 38/142 (26%), Positives = 56/142 (39%), Gaps = 17/142 (11%) Query: 142 LNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETP 201 LNS + L + RK L + D R L I F +GF+E+++P Sbjct: 172 LNSEKPKFKELESELVSRRKNDLKQMYEED---REDYLGKLERDITKFFVDRGFLEIKSP 228 Query: 202 ILQPI-----YGGATADPFKTHHNILKADMYLR--IAPELY-----LKRVLISGLTDQVF 249 IL P G + + LR +AP LY L R+L + ++F Sbjct: 229 ILIPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPGLYNYLRKLDRILPDPI--KIF 286 Query: 250 ELNRNFRNEGVSSRHNPEFTMI 271 E+ +R E H EFTM+ Sbjct: 287 EIGPCYRKESDGKEHLEEFTMV 308 >gnl|CDD|131420 TIGR02367, PylS, pyrrolysyl-tRNA synthetase. PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase. Length = 453 Score = 35.5 bits (81), Expect = 0.037 Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 14/99 (14%) Query: 185 QIRHFMEKKGFMEVETPILQP---IYGGATADPFKTHHNILKAD--MYLR--IAPELY-- 235 I F +GF+E+++PIL P I + + I + D LR +AP LY Sbjct: 248 DITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNY 307 Query: 236 ---LKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMI 271 L R L + ++FE+ +R E H EFTM+ Sbjct: 308 LRKLDRALPDPI--KIFEIGPCYRKESDGKEHLEEFTML 344 >gnl|CDD|180491 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed. Length = 529 Score = 32.6 bits (75), Expect = 0.24 Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%) Query: 458 YGMP-PASGLGLGIDRLIMLLTNAPSIRD 485 YG+ P LGLG++RL M+L A +R+ Sbjct: 312 YGIDVPVMNLGLGVERLAMILYGAEDVRE 340 >gnl|CDD|179722 PRK04036, PRK04036, DNA polymerase II small subunit; Validated. Length = 504 Score = 32.6 bits (75), Expect = 0.25 Identities = 15/88 (17%), Positives = 39/88 (44%), Gaps = 10/88 (11%) Query: 46 VREKYSH-----LQNDEKSQDMITVAGRVYSSRNSG---MFMDIHDASGKIQIFTHKDTA 97 +R + +H L+ ++ + +++ G V R++ +++ D +G + KD Sbjct: 134 IRGRVNHRPIESLKKLKRGGEEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKD-- 191 Query: 98 DQDSQNLLSMIDIGDIIGITGQVRRTKR 125 +D L + + ++IG+ G + Sbjct: 192 REDLAELADELLLDEVIGVEGTLSGDGG 219 >gnl|CDD|161893 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. Length = 294 Score = 31.9 bits (73), Expect = 0.35 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 6/61 (9%) Query: 248 VFELNRNFRNEGVSSRHNPEFTMIEAYWAYTD--YRDMMKLVEDLCHNLAKTLHGTTDIP 305 +F R FRN+ V + H PEF +E + + ++ +E+ + G T+I Sbjct: 153 IFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNVSFTNLKGFLEEFLKKMF----GETEIR 208 Query: 306 F 306 F Sbjct: 209 F 209 >gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated. Length = 1437 Score = 31.0 bits (71), Expect = 0.70 Identities = 24/121 (19%), Positives = 40/121 (33%), Gaps = 24/121 (19%) Query: 34 PAHFHRDITNAEVREKYSHLQNDEKSQDMITVAGRVYSSRNSGMFMDIHDASGKIQIFTH 93 P + I E+ + +E+ + V G V+ ++I + I T Sbjct: 214 PVQIGKKIDKEEIT-PMKEINEEERR---VVVEGYVFK-------VEIKELKSGRHILTF 262 Query: 94 KDTADQDS------------QNLLSMIDIGDIIGITGQVRR-TKRGELTVNAQKIIMLSK 140 K T S I GD + + G V+ T +L +NAQ I + Sbjct: 263 KITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQDINEIKH 322 Query: 141 A 141 Sbjct: 323 P 323 >gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728). Length = 262 Score = 30.1 bits (68), Expect = 1.3 Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 11/78 (14%) Query: 73 RNSGMFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQVRRTKRGELTVNA 132 R +FMD D + I K +DS I+ + + R + E+T Sbjct: 176 RLITIFMDYPDIDTETAILRAKTDVAEDSAA--------TIVRLVREFRAS-GDEITSGL 226 Query: 133 QKIIMLSK--ALNSIPET 148 + +M+++ IP Sbjct: 227 RASLMIAEVATQQDIPVD 244 >gnl|CDD|161882 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit. Length = 314 Score = 29.9 bits (68), Expect = 1.7 Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 6/52 (11%) Query: 176 FQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMY 227 ++ + Q++ G+ E+ TP L+ + D IL D++ Sbjct: 8 AARKEEIERQLQDVFRSWGYQEIITPTLEYL------DTLSAGGGILNEDLF 53 >gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 373 Score = 29.5 bits (67), Expect = 2.2 Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 6/30 (20%) Query: 186 IRHFMEKKGFMEVETPILQPIYGGATADPF 215 + E G + V+ PILQP A+PF Sbjct: 14 LLASFEAAGAVRVDPPILQP------AEPF 37 >gnl|CDD|179764 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha; Provisional. Length = 489 Score = 29.0 bits (66), Expect = 2.6 Identities = 11/20 (55%), Positives = 13/20 (65%) Query: 467 GLGIDRLIMLLTNAPSIRDV 486 GLGI+RL ML IRD+ Sbjct: 458 GLGIERLAMLRLGLDDIRDL 477 >gnl|CDD|183410 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit; Provisional. Length = 391 Score = 29.1 bits (66), Expect = 2.8 Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%) Query: 458 YGMP-PASGLGLGIDRLIMLL--TNAPSIRDVILFPAQ 492 +G PA+G L +DRL+ L + +D+++ P Sbjct: 300 FGRARPATGFSLDLDRLLELQLELPVEARKDLVIAPDS 337 >gnl|CDD|169396 PRK08349, PRK08349, hypothetical protein; Validated. Length = 198 Score = 28.9 bits (65), Expect = 3.0 Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 4/45 (8%) Query: 24 MLRKSLAEVYPAHFHRDITNAE-VREKYSHLQ--NDEKSQDMITV 65 MLR+ EVYP HF +D E VRE LQ + K +D + V Sbjct: 20 MLRRG-VEVYPVHFRQDEKKEEKVRELVERLQELHGGKLKDPVVV 63 >gnl|CDD|179758 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional. Length = 235 Score = 28.7 bits (65), Expect = 3.8 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 9/73 (12%) Query: 64 TVAGRVYSSRNSGMFMDI---HDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 V G+V SG +DI + A + + + + +L +DIGD I +V Sbjct: 66 LVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRP-VNVEGTDLRKYLDIGDY--IIAKV 122 Query: 121 R---RTKRGELTV 130 + RT+ LT+ Sbjct: 123 KDVDRTRDVVLTL 135 >gnl|CDD|177935 PLN02299, PLN02299, 1-aminocyclopropane-1-carboxylate oxidase. Length = 321 Score = 28.6 bits (64), Expect = 3.8 Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 19/70 (27%) Query: 263 RHNPEFTMIEAYWAYTDYRDMMK------------LVEDLCHNL-------AKTLHGTTD 303 RH PE + + +YR +MK L++ LC NL K HG+ Sbjct: 96 RHLPESNLADIPDLDDEYRKVMKDFALELEKLAEELLDLLCENLGLEKGYLKKAFHGSKG 155 Query: 304 IPFGEKVISF 313 FG KV ++ Sbjct: 156 PTFGTKVSNY 165 >gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. Length = 397 Score = 28.6 bits (65), Expect = 3.9 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 462 PASGLGLGIDRLIMLL 477 PA G +GI+RL++LL Sbjct: 295 PAVGFAIGIERLLLLL 310 >gnl|CDD|178812 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed. Length = 412 Score = 28.6 bits (65), Expect = 4.5 Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 2/22 (9%) Query: 458 YGMP--PASGLGLGIDRLIMLL 477 +G P PA G +G++RL++LL Sbjct: 290 FGGPPTPAVGFAIGVERLLLLL 311 Score = 27.8 bits (63), Expect = 6.8 Identities = 9/22 (40%), Positives = 12/22 (54%) Query: 182 LISQIRHFMEKKGFMEVETPIL 203 + IR E+ GF E+ TPI Sbjct: 24 VEDTIREVFERYGFSEIRTPIF 45 >gnl|CDD|183476 PRK12366, PRK12366, replication factor A; Reviewed. Length = 637 Score = 28.1 bits (63), Expect = 5.1 Identities = 27/112 (24%), Positives = 42/112 (37%), Gaps = 24/112 (21%) Query: 57 EKSQDMITVAGRVYSSRNSGMF------------MDIHDASGKIQIFTHKDTADQDSQNL 104 E+ Q + + GR+ N F + I D +G I++ D A L Sbjct: 70 EEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAK-----L 124 Query: 105 LSMIDIGDIIGITGQVRRTKRGELTVNAQ---KIIMLSKALNS----IPETY 149 L + GD+I I R ++ +N+ +I L K S I E Y Sbjct: 125 LKGLKEGDVIKIENARSRKWNNDVELNSGSETRIDKLEKYDESRYPIIKENY 176 >gnl|CDD|178445 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha chain. Length = 492 Score = 28.1 bits (63), Expect = 5.7 Identities = 11/24 (45%), Positives = 14/24 (58%) Query: 249 FELNRNFRNEGVSSRHNPEFTMIE 272 F ++R FRNE V H EF +E Sbjct: 346 FSIDRVFRNEAVDRTHLAEFHQVE 369 >gnl|CDD|129562 TIGR00470, sepS, O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys. Length = 533 Score = 27.9 bits (62), Expect = 6.1 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%) Query: 458 YGMP-PASGLGLGIDRLIMLLTNAPSIRDVI 487 Y + P LGLG++RL M+L +R ++ Sbjct: 311 YNIDVPVMNLGLGVERLAMILYGYEDVRAMV 341 >gnl|CDD|180051 PRK05388, argJ, bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein; Validated. Length = 395 Score = 27.8 bits (63), Expect = 6.5 Identities = 21/103 (20%), Positives = 36/103 (34%), Gaps = 42/103 (40%) Query: 279 DYRDMMKLVEDLCHNLAKTLHGTTDIPFGE---KVISFKAPFACKSMLQLVKEATGLDFM 335 D + + ++C +LAK + D GE K+I V A Sbjct: 242 DLAAFEEALTEVCQDLAKQIVR--D---GEGATKLIEVT-----------VTGA------ 279 Query: 336 LLKSDQEARVAAQSI-----------GITVENDALWGEVMMTI 367 S+++AR A++I G D WG ++ + Sbjct: 280 --ASEEDARKIAKAIANSPLVKTAIFG----EDPNWGRILAAV 316 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.319 0.134 0.383 Gapped Lambda K H 0.267 0.0713 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,168,131 Number of extensions: 536069 Number of successful extensions: 1169 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1097 Number of HSP's successfully gapped: 74 Length of query: 502 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 405 Effective length of database: 3,898,497 Effective search space: 1578891285 Effective search space used: 1578891285 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 (26.5 bits)