RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781118|ref|YP_003065531.1| lysyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (502 letters) >gnl|CDD|31383 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 502 Score = 611 bits (1577), Expect = e-175 Identities = 245/495 (49%), Positives = 333/495 (67%), Gaps = 9/495 (1%) Query: 7 PESLSSNSIEVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDEKSQDMITV- 65 ++ I VR +KL LR+ + YP F R T+A++REKY+ +E I V Sbjct: 6 EARDLNDQIAVRREKLAALREQGIDPYPNDFERTHTSADLREKYADKTKEELEALNIEVS 65 Query: 66 -AGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDS-QNLLSMIDIGDIIGITGQVR 121 AGR+ + RN G F D+ D SGKIQ++ +KD ++ + L +D+GDIIG+ G + Sbjct: 66 VAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLF 125 Query: 122 RTKRGELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSL 181 +TK GEL+V+ +++ +LSK+L +PE ++GL+D EIRYR+RYLD+I N +S+ F +RS Sbjct: 126 KTKTGELSVSVEELRLLSKSLRPLPEKFHGLTDKEIRYRQRYLDLIVNPESRQTFIKRSK 185 Query: 182 LISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLI 241 +I IR F++ +GF+EVETP+LQPI GGA A PF THHN L D+YLRIAPELYLKR+++ Sbjct: 186 IIRAIREFLDDRGFLEVETPMLQPIPGGAAARPFITHHNALDMDLYLRIAPELYLKRLIV 245 Query: 242 SGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGT 301 G ++VFE+ RNFRNEG+ + HNPEFTM+E Y AY DY D+M L E+L LAK ++GT Sbjct: 246 GGF-ERVFEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKELAKEVNGT 304 Query: 302 TDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALW- 360 T + +G + I F PF +M+ +KE G+DF L D+EA+ A+ GI VE W Sbjct: 305 TKVTYGGQEIDFSKPFKRITMVDALKEYLGVDFDDLFDDEEAKELAKKHGIEVEKYGTWG 364 Query: 361 -GEVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAF 419 G ++ +FEE +E ++ PT +TD P +ISP AK L ERFE + G EI NA+ Sbjct: 365 LGHLLNELFEELVEAKLIQPTFVTDHPVEISPLAKRHRSNPGLTERFELFIGGKEIANAY 424 Query: 420 SELNDPVEQRIRMEQQVEQSHQRG-EHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLT 478 SELNDPV+QR R E QVE+ E LDEDF++A+ YGMPP GLG+GIDRL+MLLT Sbjct: 425 SELNDPVDQRERFEAQVEEKEAGDDEAMELDEDFVEALEYGMPPTGGLGIGIDRLVMLLT 484 Query: 479 NAPSIRDVILFPAQR 493 N+PSIRDVILFPA R Sbjct: 485 NSPSIRDVILFPAMR 499 >gnl|CDD|37096 KOG1885, KOG1885, KOG1885, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 452 bits (1165), Expect = e-128 Identities = 206/502 (41%), Positives = 297/502 (59%), Gaps = 21/502 (4%) Query: 16 EVRSQKLNMLRKSLAEVYPAHFHRDITNAEVREKYSHLQNDEKSQDMI-TVAGRVYSSRN 74 ++RS+ + LR S YP FH I+ + EKY HL E + I +VAGR++S R Sbjct: 59 KIRSRAIEELRASGLNPYPHKFHVSISIPDFIEKYLHLATGEHLDNEIVSVAGRIHSKRE 118 Query: 75 SG---MFMDIHDASGKIQIF--THKDTADQDSQNLLSMIDIGDIIGITGQVRRTKRGELT 129 SG +F D+H K+Q+ K T+++D + L + GDIIG++G RTK GEL+ Sbjct: 119 SGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGYPGRTKSGELS 178 Query: 130 VNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHF 189 + +II+LS L+ +P ++GL D E RYRKRYLD+I N + + RF+ R+ +IS IR F Sbjct: 179 IIPNEIILLSPCLHMLPHEHFGLKDKETRYRKRYLDLILNPEVRDRFRIRAKIISYIRKF 238 Query: 190 MEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVF 249 ++ +GF+EVETP++ I GGATA PF THHN L D+YLRIAPELYLK +++ GL D+V+ Sbjct: 239 LDSRGFLEVETPMMNMIAGGATAKPFITHHNDLDMDLYLRIAPELYLKMLVVGGL-DRVY 297 Query: 250 ELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIP---- 305 E+ R FRNEG+ HNPEFT E Y AY DY D+M + E+L + K + G+ I Sbjct: 298 EIGRQFRNEGIDLTHNPEFTTCEFYMAYADYEDLMDMTEELLSGMVKNITGSYKITYHPN 357 Query: 306 ---FGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVENDALW-- 360 E + F PF M++ +++ G+ + + V+ Sbjct: 358 GPEEPELELDFTRPFRRIEMIEELEKELGIKLPPGSTLHTEETRELLKSLCVDEAVECPP 417 Query: 361 ----GEVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEIC 416 ++ + E +E VNPT I D P+ +SP AK + L ERFE + G EIC Sbjct: 418 PRTTARLLDKLVGEFLEPTCVNPTFIIDHPQIMSPLAKYHRSKAGLTERFELFIAGKEIC 477 Query: 417 NAFSELNDPVEQRIRMEQQVEQSHQRGEHT-ILDEDFLDAMTYGMPPASGLGLGIDRLIM 475 NA++ELNDPV+QR R EQQ + ++DEDF A+ YG+PP G G+GIDRL+M Sbjct: 478 NAYTELNDPVDQRQRFEQQARDKDAGDDEAQMVDEDFCTALEYGLPPTGGWGMGIDRLVM 537 Query: 476 LLTNAPSIRDVILFPAQRVKNG 497 LLT++ +IR+V+LFPA + ++ Sbjct: 538 LLTDSNNIREVLLFPAMKPEDR 559 >gnl|CDD|29820 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.. Length = 329 Score = 441 bits (1137), Expect = e-124 Identities = 166/329 (50%), Positives = 221/329 (67%), Gaps = 5/329 (1%) Query: 169 NSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYL 228 N + + F RS +IS IR F++ +GF+EVETP+LQPI GGA A PF THHN L D+YL Sbjct: 1 NEEVRQTFIVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGAAARPFITHHNALDMDLYL 60 Query: 229 RIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVE 288 RIAPELYLKR+++ G ++V+E+ RNFRNEG+ HNPEFTMIE Y AY DY DMM L E Sbjct: 61 RIAPELYLKRLIVGGF-ERVYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYNDMMDLTE 119 Query: 289 DLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFM---LLKSDQEARV 345 DL L K ++G T I +G K + F PF +M+ +KE TG+DF L + ++ A++ Sbjct: 120 DLFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALKEKTGIDFPELDLEQPEELAKL 179 Query: 346 AAQSIGITVENDALWGEVMMTIFEEKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVER 405 A+ I +E G+++ +FEE +E ++ PT I D P +ISP AK L ER Sbjct: 180 LAKLIKEKIEKPRTLGKLLDKLFEEFVEPTLIQPTFIIDHPVEISPLAKRHRSNPGLTER 239 Query: 406 FETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHT-ILDEDFLDAMTYGMPPAS 464 FE + G EI NA++ELNDP +QR R E+Q +Q + ++DEDF+ A+ YGMPP Sbjct: 240 FELFICGKEIANAYTELNDPFDQRERFEEQAKQKEAGDDEAMMMDEDFVTALEYGMPPTG 299 Query: 465 GLGLGIDRLIMLLTNAPSIRDVILFPAQR 493 GLG+GIDRL+MLLT++ SIRDVILFPA R Sbjct: 300 GLGIGIDRLVMLLTDSNSIRDVILFPAMR 328 >gnl|CDD|143920 pfam00152, tRNA-synt_2, tRNA synthetases class II (D, K and N). Length = 341 Score = 336 bits (863), Expect = 1e-92 Identities = 111/343 (32%), Positives = 170/343 (49%), Gaps = 12/343 (3%) Query: 154 DVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATAD 213 E R + RYLD+ + RS +I IR F++++GF+EVETPIL A Sbjct: 1 SEETRLKYRYLDLRRPKMQAN-LKLRSKIIRAIREFLDERGFLEVETPILTKSTPEGGAR 59 Query: 214 PFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGV-SSRHNPEFTMIE 272 F K + YL +P+LY + ++++G D+VF++ FR+E + + RH PEFT ++ Sbjct: 60 DFLVPKFYAK-EAYLPQSPQLYKQLLMVAGF-DRVFQIAPCFRDEDLRTDRHPPEFTQLD 117 Query: 273 AYWAYTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGL 332 ++ DY D+M L EDL + K + G T+ I PF + + ++ Sbjct: 118 LEMSFVDYEDVMDLTEDLIKYVFKEVKGKTEKGELLLGIELPEPFPRITYAEAIERYGSD 177 Query: 333 D---FMLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEEKI-EKNIVNPTHITDFPKD 388 L+ + + + ++ L G + + E + ++N+ NP +TDFP Sbjct: 178 KPDLRFGLELKDVTEIKFEDAALNGGSNKLLGALRSELGERLLGDENLDNPVFVTDFPLF 237 Query: 389 ISPFAKEVAGE-KRLVERFETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTI 447 PF + L ERF+ NG EI ++DP EQR R E+ E Sbjct: 238 KRPFYMPKDEDPPGLAERFDLVLNGGEIGGGSIRIHDPEEQRKRFEELGLD---PEEAEE 294 Query: 448 LDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 +LDA+ YGMPP G+GLG+DRL+MLLT SIR+VI FP Sbjct: 295 KFGFYLDALKYGMPPHGGIGLGLDRLVMLLTGLESIREVIAFP 337 >gnl|CDD|58337 cd00669, Asp_Lys_Asn_RS_core, Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.. Length = 269 Score = 243 bits (621), Expect = 1e-64 Identities = 117/319 (36%), Positives = 171/319 (53%), Gaps = 52/319 (16%) Query: 176 FQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRIAPELY 235 F+ RS +I IR FM+ +GF+EVETP+LQ I GGA A PF +N L D YLRI+P+L+ Sbjct: 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGAGARPFLVKYNALGLDYYLRISPQLF 60 Query: 236 LKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLA 295 KR+++ GL D+VFE+NRNFRNE + +RH PEFTM++ A+ DY D+++L E L +LA Sbjct: 61 KKRLMVGGL-DRVFEINRNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLA 119 Query: 296 KTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIGITVE 355 + + G T + +G ++ F PF + Sbjct: 120 REVLGVTAVTYGFELEDFGLPFPRLTY--------------------------------- 146 Query: 356 NDALWGEVMMTIFEEKIEKNIVNPTHITDFPKDI-SPFAKEVAGEKRLVERFETYCNGWE 414 + + P +TD+P ++ SP A + + F+ + NG E Sbjct: 147 --------------REALERYGQPLFLTDYPAEMHSPLASPHDVNPEIADAFDLFINGVE 192 Query: 415 ICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLI 474 + N S L+DP Q ++Q E+ E +L A+ YG+PP GLG+GIDRLI Sbjct: 193 VGNGSSRLHDPDIQAEVFQEQGINKEAGMEY---FEFYLKALEYGLPPHGGLGIGIDRLI 249 Query: 475 MLLTNAPSIRDVILFPAQR 493 ML+TN+P+IR+VI FP R Sbjct: 250 MLMTNSPTIREVIAFPKMR 268 >gnl|CDD|32450 COG2269, COG2269, Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 322 Score = 201 bits (513), Expect = 4e-52 Identities = 112/328 (34%), Positives = 161/328 (49%), Gaps = 30/328 (9%) Query: 175 RFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGG-ATADPFKT----HHNILKADMYLR 229 +R+ +I+ IR F ++G +EVETP L PF+T ++L Sbjct: 15 NLLKRAAIIAAIRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLH 74 Query: 230 IAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVED 289 +PE ++KR+L +G +F+L + FRNE + HNPEFTM+E Y DY +M V+D Sbjct: 75 TSPEYHMKRLLAAGSGP-IFQLGKVFRNEEMGRLHNPEFTMLEWYRVGCDYYRLMNEVDD 133 Query: 290 LCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEA-RVAAQ 348 L + + S + G+D L +D+ R AA Sbjct: 134 LLQLVLEC-----------------VEAERLSYQEAFLRYLGID--PLSADKTELREAAA 174 Query: 349 SIGITVENDALWGEVMMTIFEEKIEKNI--VNPTHITDFPKDISPFAKEVAGEKRLVERF 406 +G++ D W ++ +F E +E N+ PT + FP + A+ G+ R+ ERF Sbjct: 175 KLGLSAATDEDWDTLLQLLFVEGVEPNLGKERPTFLYHFPASQAALAQISTGDPRVAERF 234 Query: 407 ETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTI-LDEDFLDAMTYGMPPASG 465 E Y G E+ N F EL D EQR R EQ ++ +RG +DEDFL A+ MPP SG Sbjct: 235 ELYYKGIELANGFHELTDAAEQRRRFEQDNKERARRGLPQYPIDEDFLAALAR-MPPCSG 293 Query: 466 LGLGIDRLIMLLTNAPSIRDVILFPAQR 493 + LG DRL+ML A SI DVI FP R Sbjct: 294 VALGFDRLVMLALGAESIDDVIAFPVAR 321 >gnl|CDD|30367 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]. Length = 435 Score = 178 bits (454), Expect = 2e-45 Identities = 120/457 (26%), Positives = 199/457 (43%), Gaps = 48/457 (10%) Query: 46 VREKYSHLQNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQN 103 +++ H+ E +TV G V++ R+ G +F+ + D SG IQ K+ ++ Sbjct: 7 IKDIKPHVGGQE-----VTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFK 61 Query: 104 LLSMIDIGDIIGITGQVRRTKR--GELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRK 161 + + + +TG V+ + + + +KI +L +A P S++E Sbjct: 62 AKK-LTLESSVVVTGIVKASPKAPQGFELQVEKIEVLGEADPPYPIDKKEHSELETLLDN 120 Query: 162 RYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNI 221 R+LD+ + + F+ RS ++ IR F + GF EV TPI+ + FK + Sbjct: 121 RHLDLRTPKIQAV-FKIRSSILRAIREFFYENGFTEVHTPIITASATEGGGELFKV--DY 177 Query: 222 LKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGV-SSRHNPEFTMIEAYWAYTDY 280 + YL +P+LY K L + L ++VF + FR E + RH EF M++ A+ D Sbjct: 178 FDKEAYLTQSPQLY-KEALAAAL-ERVFTIGPTFRAEKSNTRRHLSEFWMLDPEMAFADL 235 Query: 281 RDMMKLVEDLCHNLAKTL--HGTTDIPF-GEKVISFKAPFACKSMLQLVKEATGLDFMLL 337 D+M L E+L L K + ++ F G K P + F + Sbjct: 236 NDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAP-------------FPRI 282 Query: 338 KSDQEARVAAQSIGITVENDALWGEVMMTIFEEKI-EKNIVNPTHITDFPKDISPF-AKE 395 EA + G WG+ + T E + E+ P +T++PK+I PF + Sbjct: 283 TYK-EAIEILEEKGFEKVE---WGDDLGTEHERYLGEEYFKPPVFVTNYPKEIKPFYMRP 338 Query: 396 VAGEKRLVERFE-TYCNGWEICNAFSELNDPVEQRI-RMEQQVEQSHQRGEHTILDEDFL 453 V F+ G EI QR + VE+ ++G E +L Sbjct: 339 DPDNPGTVASFDLLAPGGGEIIGG--------SQREHDYDLLVERIKEKGLDPESYEWYL 390 Query: 454 DAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 D YGMPP +G GLG++RL+M + +IR+ I FP Sbjct: 391 DLRKYGMPPHAGFGLGLERLVMYILGLDNIREAIPFP 427 >gnl|CDD|29821 cd00776, AsxRS_core, Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.. Length = 322 Score = 131 bits (330), Expect = 6e-31 Identities = 102/347 (29%), Positives = 156/347 (44%), Gaps = 41/347 (11%) Query: 154 DVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPIL--QPIYGGAT 211 ++E R+LD+ + I F+ RS ++ R F+ + GF EV TP + GGA Sbjct: 3 NLETLLDNRHLDLRTPKVQAI-FRIRSEVLRAFREFLRENGFTEVHTPKITSTDTEGGAE 61 Query: 212 ADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNE-GVSSRHNPEFTM 270 + YL +P+LY K +LI+ L ++V+E+ FR E + RH EF M Sbjct: 62 LFKV----SYFGKPAYLAQSPQLY-KEMLIAAL-ERVYEIGPVFRAEKSNTRRHLSEFWM 115 Query: 271 IEAYWAY-TDYRDMMKLVEDLCHNLAKTL--HGTTDIPFGEKVISFKAPFACKSMLQLVK 327 +EA A+ DY ++M L+E+L + K + ++ ++ Sbjct: 116 LEAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPL--------- 166 Query: 328 EATGLDFMLLKSDQEARVAAQSIGITVENDALWGEVMMTIFEEKIEKNIVN-PTHITDFP 386 F + D EA + G VE + WGE + T E + + + P +TD+P Sbjct: 167 ----EPFPRITYD-EAIELLREKG--VEEEVKWGEDLSTEHERLLGEIVKGDPVFVTDYP 219 Query: 387 KDISPF-AKEVAGEKRLVERFETYCNGW-EICNAFSELNDPVEQRI-RMEQQVEQSHQRG 443 K+I PF K VE F+ G EI QRI ++ E+ + G Sbjct: 220 KEIKPFYMKPDDDNPETVESFDLLMPGVGEIVGG--------SQRIHDYDELEERIKEHG 271 Query: 444 EHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 E +LD YGMPP G GLG++RL+M L +IR+ ILFP Sbjct: 272 LDPESFEWYLDLRKYGMPPHGGFGLGLERLVMWLLGLDNIREAILFP 318 >gnl|CDD|58592 cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Saccharomyces cerevisiae cytoplasmic and mitochondrial LysRSs have been shown to participate in the mitochondrial import of the only nuclear-encoded tRNA of S. cerevisiae (tRNAlysCUU). The gene for human LysRS encodes both the cytoplasmic and the mitochondrial isoforms of LysRS. In addition to their housekeeping role, human lysRS may function as a signaling molecule that activates immune cells and tomato LysRS may participate in a root-specific process possibly connected to conditions of oxidative-stress conditions or heavy metal uptake. It is known that human tRNAlys and LysRS are specifically packaged into HIV-1 suggesting a role for LysRS in tRNA packaging.. Length = 108 Score = 131 bits (330), Expect = 6e-31 Identities = 49/106 (46%), Positives = 76/106 (71%), Gaps = 3/106 (2%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDS-QNLLSMIDIGDIIGITGQ 119 ++VAGR+ S R SG F D+ D SGKIQ++ +KD ++ ++ ++D+GDIIG+TG Sbjct: 2 VSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGT 61 Query: 120 VRRTKRGELTVNAQKIIMLSKALNSIPETYYGLSDVEIRYRKRYLD 165 +TK GEL++ ++ +LSK+L +PE ++GL+DVE RYR+RYLD Sbjct: 62 PFKTKTGELSIFVKEFTLLSKSLRPLPEKFHGLTDVETRYRQRYLD 107 >gnl|CDD|73228 cd00777, AspRS_core, Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.. Length = 280 Score = 114 bits (288), Expect = 4e-26 Identities = 89/323 (27%), Positives = 141/323 (43%), Gaps = 55/323 (17%) Query: 176 FQQRSLLISQIRHFMEKKGFMEVETPILQPIYGGATAD---PFKTHHNILKADMYLRIAP 232 + RS +I IR+F++++GF+E+ETPIL D P + H A L +P Sbjct: 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEGARDFLVPSRLHPGKFYA---LPQSP 57 Query: 233 ELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDL-C 291 +L+ + +++SG D+ F++ R FR+E + + PEFT I+ ++ D D+M L+E L Sbjct: 58 QLFKQLLMVSGF-DRYFQIARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLK 116 Query: 292 HNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSIG 351 + + L PF +++ E G F Sbjct: 117 YVFKEVLGVELTTPF--PRMTYAE----------AMERYGFKF----------------- 147 Query: 352 ITVENDALWGEVMMTIFEEKIEKNIVNPTH-ITDFPKDISPFAKEVAGEKRLVERFETYC 410 LW V +FE E+ + H PK+ E E + ++ Sbjct: 148 -------LW-IVDFPLFEWDEEEGRLVSAHHPFTAPKEEDLDLLEKDPEDARAQAYDLVL 199 Query: 411 NGWEICNAFSELNDPVEQRIRMEQ---QVEQSHQRGEHTILDEDFLDAMTYGMPPASGLG 467 NG E+ ++DP Q E E++ ++ L+A YG PP G+ Sbjct: 200 NGVELGGGSIRIHDPDIQEKVFEILGLSEEEAEEKFGF------LLEAFKYGAPPHGGIA 253 Query: 468 LGIDRLIMLLTNAPSIRDVILFP 490 LG+DRL+MLLT + SIRDVI FP Sbjct: 254 LGLDRLVMLLTGSESIRDVIAFP 276 >gnl|CDD|30522 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 585 Score = 96.8 bits (241), Expect = 1e-20 Identities = 78/290 (26%), Positives = 143/290 (49%), Gaps = 42/290 (14%) Query: 39 RDITNAEVREKYSHLQNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDT 96 R E+RE SH+ +T++G V+ R+ G +F+D+ D G +Q+ + Sbjct: 2 RTHYCGELRE--SHVGQT------VTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDPE- 52 Query: 97 ADQDSQNLLSMIDIGDIIGITGQVR---------RTKRGELTVNAQKIIMLSKALNSIPE 147 ++ + S + +I +TG VR GE+ V A++I +L+ + ++P Sbjct: 53 DSPEAFEVASRLRNEFVIQVTGTVRARPEGTINPNLPTGEIEVLAEEIEVLNAS-KTLPF 111 Query: 148 TYYGLSDV--EIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQP 205 ++ EIR + RYLD+ K + RS + IR+F++ +GF+E+ETPIL Sbjct: 112 QIEDETNASEEIRLKYRYLDLRRPEMQK-NLKLRSKVTKAIRNFLDDQGFLEIETPIL-- 168 Query: 206 IYGGATAD-------PFKTHHNILKADMY-LRIAPELYLKRVLISGLTDQVFELNRNFRN 257 +T + P + H Y L +P+L+ + ++++G D+ +++ R FR+ Sbjct: 169 --TKSTPEGARDFLVPSRVH----PGKFYALPQSPQLFKQLLMVAGF-DRYYQIARCFRD 221 Query: 258 EGVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDLCHNLAKTLHGTT-DIPF 306 E + + PEFT I+ ++ D D+M+L+E L + K + G PF Sbjct: 222 EDLRADRQPEFTQIDLEMSFVDEEDVMELIEKLLRYVFKEVKGIELKTPF 271 Score = 74.8 bits (184), Expect = 5e-14 Identities = 40/122 (32%), Positives = 51/122 (41%), Gaps = 11/122 (9%) Query: 373 EKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRM 432 E V H PK E E ++ NG+E+ ++DP Q Sbjct: 440 EGRYVAAHHPFTMPKPEDLELLEADPESVRARAYDLVLNGYELGGGSIRIHDPEIQEKVF 499 Query: 433 E----QQVEQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVIL 488 E E + G L+A YG PP G+ G+DRL+MLLT A SIRDVI Sbjct: 500 EILGISPEEAEEKFGF-------LLEAFKYGAPPHGGIAFGLDRLVMLLTGAESIRDVIA 552 Query: 489 FP 490 FP Sbjct: 553 FP 554 >gnl|CDD|35774 KOG0554, KOG0554, KOG0554, Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]. Length = 446 Score = 95.7 bits (238), Expect = 2e-20 Identities = 103/458 (22%), Positives = 183/458 (39%), Gaps = 62/458 (13%) Query: 58 KSQDMITVAGRVYSSRNSG--MFMDIHDAS--GKIQIFTHKDTADQDSQNLLSMIDIGDI 113 ++ D I++ G V S R F+DI+D S +Q+ + ++ G Sbjct: 18 RAGDTISIGGWVKSVRKLKKVTFLDINDGSCPSPLQVVVDSE--------QSQLLATGTC 69 Query: 114 IGITGQVRRTKRGELTV--NAQKIIMLSKALNS--IPETYYGLSDVE----IRYRKRYLD 165 I G ++ +K + + NA+KI ++ S + + + +R R + Sbjct: 70 ISAEGVLKVSKGAKQQIELNAEKIKVVGTVDESYPLQKKKLTPEMLRDKLHLRSRTAKVG 129 Query: 166 IISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETPILQP--------IYGGATADPFKT 217 + + RS L F + F + TPI+ ++ T + Sbjct: 130 AV--------LRVRSALAFATHSFFQSHDFTYINTPIITTNDCEGAGEVFQVTTLTDYSK 181 Query: 218 HHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGV-SSRHNPEFTMIEAYWA 276 +L ++ +L+L+ + L+ V+ FR E +SRH EF M+EA A Sbjct: 182 D--FFGRPAFLTVSGQLHLE-AMACALSR-VYTFGPTFRAENSHTSRHLAEFWMLEAELA 237 Query: 277 YTDY-RDMMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFM 335 + + D+M E ++ K L I E + + P L+LV + L Sbjct: 238 FAESLDDLMSCAEAYIKHMIKYLL-EKCIEDMELMHKNEDPG-SIDRLELVAKENLLRI- 294 Query: 336 LLKSDQEAR-VAAQSIGITVENDALWGEVMMTIFEEKIEKNIVN-PTHITDFPKDISPFA 393 + EA + +++ + WG + T E+ + + P +TD+PK I PF Sbjct: 295 ---TYTEAIELLQKAVTKKFKTPPKWGIDLSTEHEKYLVEECFKKPVFVTDYPKGIKPFY 351 Query: 394 KEVAGEKRLVERFETYCNG-WEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTILDEDF 452 + + + V F+ G E+ L + + R++ E+ R E E + Sbjct: 352 MRLNDDGKTVAAFDLLVPGVGELIGG--SLREERKARLK-----ERGLTREEL----EWY 400 Query: 453 LDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 LD YG P G GLG +R++ LT +I+DVI FP Sbjct: 401 LDLRRYGSVPHGGFGLGFERMLQYLTGNDNIKDVIPFP 438 >gnl|CDD|35776 KOG0556, KOG0556, KOG0556, Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 533 Score = 94.2 bits (234), Expect = 8e-20 Identities = 102/474 (21%), Positives = 205/474 (43%), Gaps = 63/474 (13%) Query: 55 NDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLL---SMID 109 ++ + V GRV++SR G F+ + +Q + S+ ++ I Sbjct: 77 DESNDGSEVLVRGRVHTSRLKGKLCFLVLRQQGSTVQCLVAVNEDGTISKQMVKFAGSIS 136 Query: 110 IGDIIGITGQVRRTK-------RGELTVNAQKIIMLSKALNSIP---------------- 146 I+ + G V + K ++ ++ +KI ++S AL ++P Sbjct: 137 KESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISIALPNLPLQVEDASRSEPDEEKA 196 Query: 147 ---ETYYGLSDVEIRYRKRYLDIISNSDSKIRFQQRSLLISQIRHFMEKKGFMEVETP-- 201 E+ +++ R R LD+ + ++ I F+ ++ + R ++ KGF+E+ TP Sbjct: 197 AEPESTLARVNLDTRLDNRVLDLRTPTNQAI-FRIQAGVCFAFREYLRSKGFVEIHTPKL 255 Query: 202 ILQPIYGGATADPFKTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVS 261 I GGA F+ + K YL +P+LY K++ I G ++V+E+ FR E + Sbjct: 256 IGASSEGGANV--FRVSY--FKQKAYLAQSPQLY-KQMAICGDFERVYEIGPVFRAEDSN 310 Query: 262 S-RHNPEFTMIEAYWAY-TDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFAC 319 + RH EF ++ A+ Y ++M + +L + K L + +++ + + + Sbjct: 311 THRHLTEFVGLDLEMAFNEHYHEVMDTIGELFVFIFKGLRER----YAKEIETVRKQYPF 366 Query: 320 KSMLQLVKEATGLDFM-LLKSDQEARVAAQSIG-ITVENDALWGEVMMTIFEEKIEKNIV 377 + + ++ L F + +EA V ++ E++ G+++ EK Sbjct: 367 EP-FKFLEPPLRLTFKEGVAMLREAGVEMGDEDDLSTESEKKLGQLVR-------EKYDT 418 Query: 378 NPTHITDFPKDISPFAKEVAGEKRLVER-FETYCNGWEICNAFSELNDPVEQRIRMEQQV 436 + + +P + PF E ++ + G EI + ++DP E V Sbjct: 419 DFYILDKYPLAVRPFYTMPDPENPRYSNSYDFFMRGEEILSGAQRIHDP-------ELLV 471 Query: 437 EQSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 E++ + G ++D+ YG PP +G G+G++R++ML +IR LFP Sbjct: 472 ERAKEHGIDPSKISTYIDSFRYGAPPHAGGGIGLERVVMLYLGLNNIRKTSLFP 525 >gnl|CDD|35775 KOG0555, KOG0555, KOG0555, Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 545 Score = 88.9 bits (220), Expect = 3e-18 Identities = 104/448 (23%), Positives = 184/448 (41%), Gaps = 56/448 (12%) Query: 63 ITVAGRVYSSRN--SGMFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 + V G V+ R S +F+ + D +G +Q LS + G ++ Sbjct: 126 VKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQSYDALTLSTESSVTVYGTIKKL 185 Query: 121 RRTKRG----ELTVNAQKIIMLSKA---LNSIPETYYGLSDVEIRYRKRYLDIISNSDSK 173 K EL V+ +II L+ A N + E SDV++ R+L I + SK Sbjct: 186 PEGKSAPGGHELNVDYWEIIGLAPAGGFDNPLNEE----SDVDVLLDNRHLVIRGENASK 241 Query: 174 IRFQQRSLLISQIRHFMEKKGFMEVETPIL--QPIYGGATADPFKTHHNILKADMYLRIA 231 + + R+ L+ +R ++G+ EV P + + GG+T FK + + YL + Sbjct: 242 V-LKARAALLRAMRDHYFERGYTEVTPPTMVQTQVEGGSTL--FKL--DYYGEEAYLTQS 296 Query: 232 PELYLKRVLISGLTDQVFELNRNFRNE-GVSSRHNPEFTMIEAYWAYTDYRDMMKLVEDL 290 +LYL+ L + V+ + +++R E + RH E+T +EA A+ + D++ +E L Sbjct: 297 SQLYLETCLPA--LGDVYCIQQSYRAEKSRTRRHLSEYTHVEAECAFLTFDDLLDRIEAL 354 Query: 291 CHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFMLLKSDQEARVAAQSI 350 + ++ + P + F +A F + +A + Sbjct: 355 ---VCDSVDRLLEDPIAPLIKQLNPDF----------KAPKRPFKRMNY-SDAIEWLKEH 400 Query: 351 GITVEN--DALWGEVMMTIFEEKIEKNIVNPTHITDFPKDISPF-AKEVAGEKRLVERFE 407 + E+ D +G+ + E K+ I P +T FP +I F K + RL E + Sbjct: 401 DVKKEDGTDFEFGDDIPEAAERKMTDTIGVPIFLTRFPVEIKSFYMKRCEDDPRLTESVD 460 Query: 408 T-YCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEHTILDED----FLDAMTYGMPP 462 N EI RI +++ +R +D D + D YG P Sbjct: 461 VLMPNVGEIVGG--------SMRIDDSEELLAGFKREG---IDPDPYYWYTDQRKYGTCP 509 Query: 463 ASGLGLGIDRLIMLLTNAPSIRDVILFP 490 G GLG++R + L + +R+V L+P Sbjct: 510 HGGYGLGLERFLAWLCDRYHVREVCLYP 537 >gnl|CDD|37622 KOG2411, KOG2411, KOG2411, Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis]. Length = 628 Score = 87.0 bits (215), Expect = 1e-17 Identities = 69/247 (27%), Positives = 122/247 (49%), Gaps = 23/247 (9%) Query: 63 ITVAGRVYSSRNSGM--FMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 + + G + R M F ++ DA G +Q D+ +Q L + + + D++ + G V Sbjct: 50 VVLCGWLELHRVHKMLTFFNLRDAYGIVQQLLSPDSFPL-AQKLENDVPLEDVVQVEGTV 108 Query: 121 R---------RTKRGELTVNAQKIIMLSKALNSIP---ETYYGLSDV---EIRYRKRYLD 165 + K G + V A+K+ +L+ +P + L D+ IR R RYLD Sbjct: 109 VSRPNESINSKMKTGFVEVVAEKVEVLNPVNKKLPFEVTDFKELDDLAGERIRLRFRYLD 168 Query: 166 IISNSDSKIRFQQRSLLISQIRHFM-EKKGFMEVETPIL-QPIYGGATADPFKTHHNILK 223 + + + RS ++ +IR ++ + GF+EVETP L + GGA T K Sbjct: 169 LRRP-KMQNNLRLRSNVVKKIRRYLNNRHGFVEVETPTLFKRTPGGAREFVVPTRTPRGK 227 Query: 224 ADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDYRDM 283 L +P+ + K++L+ D+ +++ R FR+E + + PEFT ++ ++TD D+ Sbjct: 228 F-YALPQSPQQF-KQLLMVSGIDRYYQIARCFRDEDLRADRQPEFTQVDMEMSFTDQEDI 285 Query: 284 MKLVEDL 290 MKL+EDL Sbjct: 286 MKLIEDL 292 Score = 63.9 bits (155), Expect = 9e-11 Identities = 36/105 (34%), Positives = 52/105 (49%), Gaps = 6/105 (5%) Query: 386 PKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRMEQQVEQSHQRGEH 445 PKDI EK + ++ NG E+ +++P QR +E ++ Sbjct: 497 PKDIDLLESA--PEKIRGQHYDLVVNGVELGGGSIRIHNPDIQRYVLEDILKIPEDA--- 551 Query: 446 TILDEDFLDAMTYGMPPASGLGLGIDRLIMLLTNAPSIRDVILFP 490 L+A+ G PP G+ LG+DRL+ +LT APSIRDVI FP Sbjct: 552 -ESKGHLLNALDMGAPPHGGIALGLDRLVAMLTGAPSIRDVIAFP 595 >gnl|CDD|29813 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.. Length = 211 Score = 72.0 bits (176), Expect = 4e-13 Identities = 44/158 (27%), Positives = 66/158 (41%), Gaps = 19/158 (12%) Query: 178 QRSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFK----THHNILKADMYLRIAPE 233 RS + ++R FM + GF EVETPI++ A + D+YLR E Sbjct: 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEEDLYLRPTLE 60 Query: 234 LYLKRVLISGLTDQ---VFELNRNFRNEGVSS--RHNPEFTMIEAYWAYTD------YRD 282 L R+ +S + + E+ FRNEG R EFT +E D + + Sbjct: 61 PGLVRLFVSHIRKLPLRLAEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGEEASEFEE 120 Query: 283 MMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFACK 320 +++L E+ L + L DI F EK +P Sbjct: 121 LIELTEE----LLRALGIKLDIVFVEKTPGEFSPGGAG 154 Score = 27.7 bits (61), Expect = 8.2 Identities = 18/96 (18%), Positives = 31/96 (32%), Gaps = 21/96 (21%) Query: 378 NPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICNAFSELNDPVEQRIRMEQQVE 437 + + P + SP E +E G EI + + + Sbjct: 137 DIVFVEKTPGEFSPGGAGPGFE---IEVDHPEGRGLEIGSGG-----------YRQDEQA 182 Query: 438 QSHQRGEHTILDEDFLDAMTYGMPPASGLGLGIDRL 473 ++ +A+ Y PP G GLG++RL Sbjct: 183 RAADLYFL-------DEALEYRYPPTIGFGLGLERL 211 >gnl|CDD|58585 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like AspRSs which are non-discriminating and can charge both tRNAAsp and tRNAAsn. E. coli cells have two isoforms of LysRSs (LysS and LysU) encoded by two distinct genes, which are differentially regulated. The cytoplasmic and the mitochondrial isoforms of human LysRS are encoded by a single gene. Yeast cytoplasmic and mitochondrial LysRSs participate in mitochondrial import of cytoplasmic tRNAlysCUU. In addition to their housekeeping role, human LysRS may function as a signaling molecule that activates immune cells. Tomato LysRS may participate in a process possibly connected to conditions of oxidative-stress conditions or heavy metal uptake. It is known that human tRNAlys and LysRS are specifically packaged into HIV-1 suggesting a role for LysRS in tRNA packaging. AsnRS is immunodominant antigen of the filarial nematode Brugia malayai and is of interest as a target for anti-parasitic drug design. Human AsnRS has been shown to be a pro-inflammatory chemokine which interacts with CCR3 chemokine receptors on T cells, immature dendritic cells and macrophages.. Length = 85 Score = 62.6 bits (152), Expect = 2e-10 Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 8/85 (9%) Query: 63 ITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQV 120 +T+AG V+S R+ G +F+D+ D SG +Q+ +K+ + + ++G+TG V Sbjct: 2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELG-EFFEEAEKLRTESVVGVTGTV 60 Query: 121 RRTKR-----GELTVNAQKIIMLSK 140 + GE+ + A+++ +LSK Sbjct: 61 VKRPEGNLATGEIELQAEELEVLSK 85 >gnl|CDD|144799 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Length = 75 Score = 60.7 bits (148), Expect = 9e-10 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 7/79 (8%) Query: 63 ITVAGRVYSSRNSG---MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITGQ 119 +TVAGRV S R SG F+ + D +G IQ+ K+ A++ ++ L GD++ +TG+ Sbjct: 1 VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKL----KEGDVVLVTGK 56 Query: 120 VRRTKRGELTVNAQKIIML 138 V++ GEL + ++I +L Sbjct: 57 VKKRPGGELELVVEEIEVL 75 >gnl|CDD|58587 cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with mitochondrial protein synthesis. Human mtAspRS participates in mitochondrial biosynthesis; this enzyme been shown to charge E.coli native tRNAsp in addition to in vitro transcribed human mitochondrial tRNAsp. T. thermophilus is rare among bacteria in having both a D_AspRS and a ND_AspRS. H.pylori ND-AspRS can charge both tRNAASp and tRNAAsn, it is fractionally more efficient at aminoacylating tRNAAsp over tRNAAsn. The H.pylori genome does not contain AsnRS.. Length = 135 Score = 49.0 bits (117), Expect = 3e-06 Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 22/140 (15%) Query: 39 RDITNAEVREKYSHLQNDEKSQDMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDT 96 R E+RE SH+ + +T+ G V R+ G +F+D+ D G +Q+ + Sbjct: 1 RTHYCGELRE--SHVGQE------VTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPE- 51 Query: 97 ADQDSQNLLSMIDIGDIIGITGQVR---------RTKRGELTVNAQKIIMLSKALN-SIP 146 + L + +I +TG+VR + GE+ V A ++ +L+KA Sbjct: 52 -EAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNKAKTLPFE 110 Query: 147 ETYYGLSDVEIRYRKRYLDI 166 E+R + RYLD+ Sbjct: 111 IDDDVNVSEELRLKYRYLDL 130 >gnl|CDD|29807 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.. Length = 218 Score = 41.3 bits (97), Expect = 6e-04 Identities = 28/128 (21%), Positives = 47/128 (36%), Gaps = 13/128 (10%) Query: 180 SLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNIL-KADMYLRIAPELYLKR 238 + +I +I GF EVE P ++ + A H D + P L R Sbjct: 4 NKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQDTFYINDPARLLLR 63 Query: 239 VLISGLT----------DQVFELNRNFRNEGVSSRHNPEFTMIEAYWAYTD--YRDMMKL 286 S + ++F + R +RN+ + + H PEF IE + D+ Sbjct: 64 THTSAVQARALAKLKPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGT 123 Query: 287 VEDLCHNL 294 +E+ L Sbjct: 124 LEEFAKEL 131 Score = 29.7 bits (67), Expect = 1.7 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 467 GLGIDRLIMLLTNAPSIRD 485 G+G++RL ML P IR Sbjct: 193 GIGLERLAMLKYGIPDIRL 211 >gnl|CDD|58586 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.. Length = 108 Score = 40.6 bits (95), Expect = 0.001 Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 4/90 (4%) Query: 61 DMITVAGRVYSSRNSG--MFMDIHDASGKIQIFTHKDTADQDSQNLLSMIDIGDIIGITG 118 + +TVAG V+ R+ G F+ + D G +Q+ K D++ + + +I +TG Sbjct: 13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTG 72 Query: 119 QVRRTKR--GELTVNAQKIIMLSKALNSIP 146 V+ + + + ++I +LS+A +P Sbjct: 73 TVKAEPKAPNGVEIIPEEIEVLSEAKTPLP 102 >gnl|CDD|144252 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G, H, P, S and T). Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. Length = 170 Score = 37.6 bits (88), Expect = 0.009 Identities = 34/142 (23%), Positives = 59/142 (41%), Gaps = 30/142 (21%) Query: 179 RSLLISQIRHFMEKKGFMEVETPILQP-----IYGGAT--ADPFKTHHNILKADMYLRIA 231 R+ L + IR ++ G+ EV+TPIL+P G D + ++YLR Sbjct: 2 RNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDEMYRFKDRGGEELYLR-- 59 Query: 232 PE------LYLKRVLISG--LTDQVFELNRNFRNEGVSSR-----HNPEFTMIEAYWAYT 278 P K ++S L +++++ FR E R EFT ++A T Sbjct: 60 PTAEVGITRLFKNEILSYRDLPLKLYQIGPCFRYEARPRRGLGRVR--EFTQVDAEIFGT 117 Query: 279 D------YRDMMKLVEDLCHNL 294 +++KL E++ +L Sbjct: 118 PEQSEEEDEELLKLAEEILQDL 139 >gnl|CDD|30366 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]. Length = 335 Score = 34.8 bits (80), Expect = 0.059 Identities = 29/134 (21%), Positives = 48/134 (35%), Gaps = 23/134 (17%) Query: 182 LISQIRHFMEKKGFMEVETPILQPIYGGATA------DPFKTHHNILKADMYLRIAPELY 235 I +I GF EVE P ++ + A P + + YL+ E Sbjct: 116 TIEEIEDIFLGMGFTEVEGPEIETDFYNFDALNIPQDHPARDMQDTF----YLKDDREKL 171 Query: 236 LKRVLISGLTDQ-----------VFELNRNFRNEGVSSRHNPEFTMIEAYWAYTD--YRD 282 L R S + + +F R +RN+ V + H+PEF IE + + D Sbjct: 172 LLRTHTSPVQARTLAENAKIPIKIFSPGRVYRNDTVDATHSPEFHQIEGLVVDKNISFAD 231 Query: 283 MMKLVEDLCHNLAK 296 + +E+ Sbjct: 232 LKGTLEEFAKKFFG 245 Score = 31.3 bits (71), Expect = 0.69 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%) Query: 447 ILDEDFLDAMTYGMPPASGL--GLGIDRLIMLLTNAPSIRD 485 ++ + L+A+ SG GLG++RL ML P IRD Sbjct: 284 MVHPNVLEAVGIDPEEYSGFAFGLGLERLAMLKYGIPDIRD 324 >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 31.4 bits (71), Expect = 0.59 Identities = 46/234 (19%), Positives = 82/234 (35%), Gaps = 46/234 (19%) Query: 179 RSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKT--HHNILKADMYLRIAPE--- 233 R+LL +R + G+ EV+TP+L A + ++ H + K DM+L + + Sbjct: 223 RNLLEDYVRTKLRSYGYQEVKTPVL------ADLELWELSGHWDNYKEDMFLTESDDREY 276 Query: 234 -----------LYLKRVLIS--GLTDQVFELNRNFRNEGVSSRHNP----EFTMIEAYWA 276 L K L S L ++ E +R E + H FT +A+ Sbjct: 277 ALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIF 336 Query: 277 YTDYRDMMKLVEDLCHNLAKTLHGTTDIPFGEKVISFKAPFACKSMLQLVKEATGLDFML 336 T + + L ++ E +S + F G D M Sbjct: 337 CTPDQIKDEFKG--ILELILEVYKDFGFTDYEVKLSTRPKFI------------GSDEMW 382 Query: 337 LKSDQEARVAAQSIGITVEND----ALWGEVMMTIFEEKIEKNIVNPTHITDFP 386 K++ R A + IG+ + A +G + ++ + + T DF Sbjct: 383 DKAEAALREALKEIGVEYVEEPGEGAFYGPKIDFQVKDALGREWQLGTIQLDFN 436 >gnl|CDD|29816 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.. Length = 298 Score = 31.3 bits (71), Expect = 0.67 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 10/63 (15%) Query: 179 RSLLISQIRHFMEKKGFMEVETPILQPIYGGATADPFKT--HHNILKADMYLRIAP--EL 234 R+ L +R K+G+ EVETPI+ + ++T H + + +M+ E Sbjct: 33 RNELEDFLRELQRKRGYQEVETPII------YNKELWETSGHWDHYRENMFPFEEEDEEY 86 Query: 235 YLK 237 LK Sbjct: 87 GLK 89 >gnl|CDD|144850 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain. Length = 243 Score = 31.0 bits (71), Expect = 0.79 Identities = 10/21 (47%), Positives = 12/21 (57%) Query: 465 GLGLGIDRLIMLLTNAPSIRD 485 GLG++RL ML IRD Sbjct: 211 AFGLGVERLAMLKYGIDDIRD 231 Score = 27.9 bits (63), Expect = 6.3 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%) Query: 248 VFELNRNFRNEGVSSRHNPEFTMIEAYWAYTDY--RDMMKLVEDLCHNLA 295 +F + R FR + V + H PEF +E + D+ ++E+ Sbjct: 103 IFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVSFADLKGVLEEFLRKFF 152 >gnl|CDD|32207 COG2024, COG2024, Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]. Length = 536 Score = 30.7 bits (69), Expect = 0.86 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%) Query: 458 YGMP-PASGLGLGIDRLIMLLTNAPSIRDVI 487 YG+ P LGLG++RL M+L A +R ++ Sbjct: 319 YGIDYPVMNLGLGVERLAMILHGADDVRSMV 349 >gnl|CDD|37995 KOG2784, KOG2784, KOG2784, Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]. Length = 483 Score = 30.0 bits (67), Expect = 1.8 Identities = 22/99 (22%), Positives = 38/99 (38%), Gaps = 16/99 (16%) Query: 216 KTHHNILKADMYLRIAPELYLKRVLISGLTDQVFELNRNFRNEGVSSRHNPEFTMIEAYW 275 +TH + A M R+A + + + F ++R FRNE V + H EF +E Sbjct: 312 RTHTTAVSARMLYRLAKKGFKPA--------KYFSIDRVFRNETVDATHLAEFHQVEGVI 363 Query: 276 AYTDYR----DMMKLVEDL--CHNLAKTLHGTTDIPFGE 308 A D D++ ++ + P+ E Sbjct: 364 A--DKGLTLGDLIGILMEFFTKLGATNLRFKPAYNPYTE 400 >gnl|CDD|143468 cd07150, ALDH_VaniDH_like, Pseudomonas putida vanillin dehydrogenase-like. Vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid and other related sequences are included in this CD. The E. coli vanillin dehydrogenase (LigV) preferred NAD+ to NADP+ and exhibited a broad substrate preference, including vanillin, benzaldehyde, protocatechualdehyde, m-anisaldehyde, and p-hydroxybenzaldehyde. Length = 451 Score = 29.2 bits (66), Expect = 2.6 Identities = 13/48 (27%), Positives = 19/48 (39%) Query: 370 EKIEKNIVNPTHITDFPKDISPFAKEVAGEKRLVERFETYCNGWEICN 417 K + N PT +TD D+ F +E G V + E+ N Sbjct: 331 GKYDGNFYQPTVLTDVTPDMRIFREETFGPVTSVIPAKDAEEALELAN 378 >gnl|CDD|73227 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with GlyRS, Pol gamma b lacks conservation of several class II functional residues.. Length = 254 Score = 28.2 bits (63), Expect = 4.7 Identities = 29/112 (25%), Positives = 46/112 (41%), Gaps = 27/112 (24%) Query: 182 LISQIRHFM--EKKGFMEVETPILQPIYGGATADPFKTHH---NILKADMYLRIAPE--- 233 + S R E++ +E+++PI+ P FKT YLR PE Sbjct: 38 IKSAWRKSFVLEEEDMLEIDSPIITP------ELMFKTSIGPVESGGNLGYLR--PETAQ 89 Query: 234 ---LYLKRVLISG---LTDQVFELNRNFRNEGVSSRHN----PEFTMIEAYW 275 + K +L L V ++ ++FRNE +S R+ EFT E + Sbjct: 90 GIFVNFKNLLEFNRRKLPFGVAQIGKSFRNE-ISPRNGLFRVREFTQAEIEF 140 >gnl|CDD|33500 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]. Length = 390 Score = 27.6 bits (61), Expect = 8.6 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 9/47 (19%) Query: 184 SQIRHFMEKKGFMEVETPILQPIYGGATADPFKTHHNILKADMYLRI 230 Q+ G+ VETP L+P ADP D+ R+ Sbjct: 25 DQLLALFRAWGYERVETPTLEP------ADPLLDG---AGEDLRRRL 62 >gnl|CDD|38040 KOG2829, KOG2829, KOG2829, E2F-like protein [Transcription]. Length = 326 Score = 27.3 bits (60), Expect = 9.1 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 1/56 (1%) Query: 50 YSHLQNDEKSQDMITVAGRVYSSRNSGMFMDIHDASGK-IQIFTHKDTADQDSQNL 104 YSH+ +E+ D + RVY + N M M+I K I+ T+ QD L Sbjct: 82 YSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKDKKEIRWIGLPATSSQDVSEL 137 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 0.319 0.134 0.383 Gapped Lambda K H 0.267 0.0648 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,943,937 Number of extensions: 318610 Number of successful extensions: 785 Number of sequences better than 10.0: 1 Number of HSP's gapped: 731 Number of HSP's successfully gapped: 50 Length of query: 502 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 404 Effective length of database: 4,146,055 Effective search space: 1675006220 Effective search space used: 1675006220 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 (26.7 bits)