RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781004|ref|YP_003065417.1| threonyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (652 letters) >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 701 bits (1811), Expect = 0.0 Identities = 301/610 (49%), Positives = 411/610 (67%), Gaps = 33/610 (5%) Query: 37 KAVAVAINGKVCDLSDPVREGSIEIITPEDPRSLAVIRHSCAHIMAEAVQSIWPEVQVAI 96 KA+A+ ++G++ DL D EIIT ED L +IRHSCAH++A+AV+ ++P+V I Sbjct: 1 KALAIHVDGEL-DLKD-------EIITAEDEEGLEIIRHSCAHVLAQAVKRLYPDV--TI 50 Query: 97 GPIIEDGFYYDFDKEQPFSSDELAQIEKKMQEIIARDSPFLKQYLSHEKARELFESKKEA 156 GP+IE+GFYYDFD ++P + ++L +IEK+M+EI + P ++ +S E+AR F Sbjct: 51 GPVIEEGFYYDFDVKEPITPEDLLKIEKEMKEIAKENLPIEREVVSREEARAPFGP---- 106 Query: 157 YKVEILESIPAKENVTLYRQGEWFDLCRGPHVRSTGQVKKFFKLMKVAGAYWRGDSNRPM 216 YK E+++ ++ Y QGE+ DLCRGPHV STG++ FKL+K+AGAYWRGD N M Sbjct: 107 YKAELIDCKG--HPLSEYSQGEFVDLCRGPHVPSTGKI--AFKLLKLAGAYWRGDENNEM 162 Query: 217 LSRIYGTAWNTQQELTQYLYFLEESEKRDHRKLAREMDLFHI-AEDGSGVIFWHRKGWKI 275 L RIYGTA+ ++EL YL LEE++KRDHRKL +E+DLF E+G G+ FWH KG I Sbjct: 163 LQRIYGTAFADKKELEAYLKRLEEAKKRDHRKLGKELDLFSFSPEEGPGLPFWHPKGATI 222 Query: 276 FQTLISYMRRK-IKDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTF 334 L Y+R K Y+E+ TP + D LW+ SGHWD+Y+ +MF T D R + Sbjct: 223 RNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWDNYKEDMFL------TESDDREY 276 Query: 335 ALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVF 394 ALKPMNCPGH+ +F GL+SYRELP+RLAEFG VYR E SG+LHGLMRVRGFTQDDAH+F Sbjct: 277 ALKPMNCPGHILIFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIF 336 Query: 395 CTKEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLDT 454 CT +Q+ +E I LI+ +YKDFGF VKLSTRP K +GSD +WD AE ++ L Sbjct: 337 CTPDQIKDEFKGILELILEVYKDFGFTDYEVKLSTRP-KFIGSDEMWDKAEAALREALKE 395 Query: 455 IKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGTIQVDFNLPSRFNAFYVNSH 514 I + GEGAFYGPK ++ +KDA+GR+WQ GTIQ+DFNLP RF+ YV+ Sbjct: 396 I------GVEYVEEPGEGAFYGPKIDFQVKDALGREWQLGTIQLDFNLPERFDLEYVDED 449 Query: 515 SEKCHPVMIHRAVFGSIERFIGIMIENFKGNLPLWLSPIQAIVTTITSSAVEYAQEIANL 574 EK PV+IHRA+ GSIERFIGI++E++ G LP WL+P+Q V + ++YA+E+A Sbjct: 450 GEKKRPVIIHRAILGSIERFIGILLEHYAGALPTWLAPVQVRVIPVADEHLDYAKEVAEK 509 Query: 575 LKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEASERSIGIRRFGSTTTQKVSL 634 L+ + ++ D RNE + KIRE +KIP +I+ GDKE ++ +RR G + ++L Sbjct: 510 LRKAGIRVDIDDRNEKLGKKIREAGTQKIPYVIVVGDKEVETGTVVVRRRGGKQQKSMTL 569 Query: 635 LDAIPILTKE 644 + + L KE Sbjct: 570 EELVEELKKE 579 >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 = 414 bits (1067), Expect = e-116 Identities = 153/310 (49%), Positives = 199/310 (64%), Gaps = 13/310 (4%) Query: 244 RDHRKLAREMDLFHIAEDGSGVIFWHRKGWKIFQTLISYMRRK-IKDDYEEINTPQVLDQ 302 R F E G G+ FW KG I L ++R K Y+E+ TP + ++ Sbjct: 1 DHRRLGGELELFFFFDEAGPGLPFWLPKGAIIRNELEDFLRELQRKRGYQEVETPIIYNK 60 Query: 303 HLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRL 362 LW+ SGHWD YR NMF + D + LKPMNCPGH +F +SYR+LP+RL Sbjct: 61 ELWETSGHWDHYRENMFPFEEED------EEYGLKPMNCPGHCLIFKSKPRSYRDLPLRL 114 Query: 363 AEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFCTKEQMFNECLKIHNLIISIYKDFGFEK 422 AEFG+V+R E SG+LHGL RVRGFTQDDAH+FCT +Q+ E + +LI +Y DFGF Sbjct: 115 AEFGTVHRYEQSGALHGLTRVRGFTQDDAHIFCTPDQIKEEIKGVLDLIKEVYSDFGFFD 174 Query: 423 IMVKLSTRPEKRVGSDALWDDAENIMKGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYI 482 V+LSTRPEK +GSD +W+ AE ++ L+ I + + GEGAFYGPK ++ Sbjct: 175 YKVELSTRPEKFIGSDEVWEKAEAALREALEEI------GLPYEINEGEGAFYGPKIDFH 228 Query: 483 LKDAIGRDWQCGTIQVDFNLPSRFNAFYVNSHSEKCHPVMIHRAVFGSIERFIGIMIENF 542 +KDA+GR+WQC TIQ+DFNLP RF+ Y+ EK PVMIHRA+ GSIERFIGI+IE++ Sbjct: 229 VKDALGREWQCSTIQLDFNLPERFDLTYIGEDGEKKRPVMIHRAILGSIERFIGILIEHY 288 Query: 543 KGNLPLWLSP 552 G PLWL+P Sbjct: 289 AGKFPLWLAP 298 >gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 378 bits (973), Expect = e-105 Identities = 192/526 (36%), Positives = 285/526 (54%), Gaps = 41/526 (7%) Query: 102 DGFYYDFDKEQPFSSDELAQIEKKMQEIIARDSPFLKQYLSHEKARELFESKKEAYKVEI 161 +G +D D+ P D L E++ D K H A L E+ ++ Y + Sbjct: 40 NGVLWDLDR--PLEGDCL--------ELLKFDDDEGKDVFWHSSAHVLGEALEQEYGAHL 89 Query: 162 LESIPAKENV--TLYRQ--GEWFDLCRGPHVRSTGQVKKFFKLMKVAGAYWRGDSNRPML 217 P +E + + F PH+R TG++K F K++K + AYW GDS Sbjct: 90 CIGPPIEEGFYYDMLDEISSNDFPSIEAPHIRHTGKIKAF-KILKNSSAYWEGDS----- 143 Query: 218 SRIYGTAWNTQQELTQYLYFLEESEKRDHRKLAREMDLFHIAEDGSGVIFWHRKGWKIFQ 277 + ++L ++ F EE++KRDHRK+ +E +LF E G F+ G +I+ Sbjct: 144 -------FPDPKQLKEWEKFQEEAKKRDHRKIGKEQELFFFHELSPGSCFFLPHGTRIYN 196 Query: 278 TLISYMRRKI-KDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFAL 336 TL+ ++R + K + E+ TP + ++ LW+ SGHW +Y NMF + + FAL Sbjct: 197 TLVDFIRAEYRKRGFTEVITPNIYNKKLWETSGHWQNYSENMFKFEVEKEE------FAL 250 Query: 337 KPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFCT 396 KPMNCPGH +F H +SYRELP+R A+FG ++RNE SG+L GL RVR F QDDAH+FCT Sbjct: 251 KPMNCPGHCLMFAHRDRSYRELPLRFADFGVLHRNEASGALSGLTRVRRFQQDDAHIFCT 310 Query: 397 KEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLDTIK 456 +Q+ E + + +Y FGF + LSTRPEK +G WD+AE ++ L+ + Sbjct: 311 PDQVKEEIKGCLDFLDYVYGVFGF-TFKLNLSTRPEKFLGDLETWDEAEFKLEEALN--E 367 Query: 457 NSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGTIQVDFNLPSRFNAFYVNSHSE 516 + +N G +GAFYGPK + L DA+GR QC TIQ+DF LP RF+ Y + Sbjct: 368 SGEPWVLNPG----DGAFYGPKIDITLDDALGRKHQCATIQLDFQLPIRFDLEYETEDGD 423 Query: 517 KCHPVMIHRAVFGSIERFIGIMIENFKGNLPLWLSPIQAIVTTITSSAVEYAQEIANLLK 576 PVMIHRA+ GS+ER I I++E++ G P WLSP QA+V ++ ++YA + L+ Sbjct: 424 LERPVMIHRAILGSVERMIAILLESYGGKWPFWLSPRQAVVIPVSEGPLDYATSVQKQLE 483 Query: 577 SHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEASERSIGIR 622 ++ D + T+ KIR + I + GDKE + +R Sbjct: 484 EAGFYVDLDPTDSTLRKKIRNAQLAHYNFIFVVGDKEVETGRVNVR 529 Score = 75.4 bits (185), Expect = 5e-14 Identities = 52/201 (25%), Positives = 86/201 (42%), Gaps = 18/201 (8%) Query: 5 IKLTFPDGSIKNFPV-HATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVREGSIEIIT 63 I + PDG + T D+A S+ LA AV +NG + DL P+ +E++ Sbjct: 1 IIIVLPDGKVVEGVSWETTPYDIACQ-SKGLADDAVIAKVNGVLWDLDRPLEGDCLELLK 59 Query: 64 PEDPRSLAVIRHSCAHIMAEAVQSIWPEVQVAIGPIIEDGFYYDFDKEQPFSSDELAQIE 123 +D V HS AH++ EA++ + + IGP IE+GFYYD E SS++ IE Sbjct: 60 FDDDEGKDVFWHSSAHVLGEALEQEYG-AHLCIGPPIEEGFYYDMLDE--ISSNDFPSIE 116 Query: 124 ----------KKMQEIIARDSPFLKQYLSHEKARELFESKKEAYKVEILESIPAKENVTL 173 K + + + + K + +E +E K I ++ + Sbjct: 117 APHIRHTGKIKAFKILKNSSAYWEGDSFPDPKQLKEWEKFQEEAKKRDHRKIGKEQELFF 176 Query: 174 YRQ---GEWFDLCRGPHVRST 191 + + G F L G + +T Sbjct: 177 FHELSPGSCFFLPHGTRIYNT 197 >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 = 152 bits (386), Expect = 3e-37 Identities = 53/170 (31%), Positives = 83/170 (48%), Gaps = 8/170 (4%) Query: 275 IFQTLISYMRRK-IKDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRT 333 + L +++R + Y+E++TP + + LW+ SGHWD Y M+ + D + Sbjct: 1 LRNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDEMY--RFKD---RGGEE 55 Query: 334 FALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHV 393 L+P G +F + + SYR+LP++L + G +R E GL RVR FTQ DA + Sbjct: 56 LYLRPTAEVGITRLFKNEILSYRDLPLKLYQIGPCFRYEA-RPRRGLGRVREFTQVDAEI 114 Query: 394 FCTKEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDD 443 F T EQ E ++ L I +D G V L+TR + + D Sbjct: 115 FGTPEQSEEEDEELLKLAEEILQDLGL-PYRVVLNTRGDLGGYASKTGDL 163 >gnl|CDD|29810 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.. Length = 235 Score = 136 bits (344), Expect = 2e-32 Identities = 56/273 (20%), Positives = 101/273 (36%), Gaps = 43/273 (15%) Query: 272 GWKIFQTLISYMRRKIKDD-YEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKD 330 G +++ L ++ ++ + Y+EI P + L+ + GH D YR M+ + ++D Sbjct: 1 GTALWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRD 60 Query: 331 LRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDD 390 L+P C +F+ + SYR LP+RL + G +R+EPSG GLMRVR F Q + Sbjct: 61 -TDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRHEPSGR-RGLMRVREFRQVE 118 Query: 391 AHVFCTKEQMFNECLKIHNLIISIYKDFG---FEKIMVKLSTRPEKRVGSDALWDDAENI 447 VF E+ + + + ++ + V ++ P G Sbjct: 119 YVVFGEPEEA----EEERREWLELAEEIARELGLPVRVVVADDPFFGRGGK--------- 165 Query: 448 MKGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAI-GRDWQCGTIQVDFNLPSRF 506 G A E+ L + GR + + +L Sbjct: 166 ---------------------RGLDAGRETVVEFELLLPLPGRAKETAVGSANVHLDHFG 204 Query: 507 NAFYVNSHSEKCHPVMIHRAVFGSIERFIGIMI 539 +F ++ G ER + ++ Sbjct: 205 ASFKIDEDGGGRAHTGCGG--AGGEERLVLALL 235 >gnl|CDD|29800 cd00860, ThrRS_anticodon, ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.. Length = 91 Score = 94.4 bits (235), Expect = 9e-20 Identities = 30/87 (34%), Positives = 49/87 (56%) Query: 552 PIQAIVTTITSSAVEYAQEIANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGD 611 P+Q +V +T ++YA+E+A L + +E D RNE + KIRE ++KIP I++ GD Sbjct: 1 PVQVVVIPVTDEHLDYAKEVAKKLSDAGIRVEVDLRNEKLGKKIREAQLQKIPYILVVGD 60 Query: 612 KEASERSIGIRRFGSTTTQKVSLLDAI 638 KE ++ +R +SL + I Sbjct: 61 KEVETGTVSVRTRDGGDLGSMSLDEFI 87 >gnl|CDD|30791 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 500 Score = 85.7 bits (212), Expect = 3e-17 Identities = 77/383 (20%), Positives = 144/383 (37%), Gaps = 67/383 (17%) Query: 258 IAEDGSGVIFWHRKGWKIFQTLISYMRRKI-KDDYEEINTPQVLDQHLWQQSGHWDSYRA 316 I + G+ W G ++ + + + +R ++ K +E+ P ++ LW++SG W+ + Sbjct: 32 IRKPVKGLYVWLPLGLRVLEKIENIIREEMDKIGAQEVLFPTLIPAELWKESGRWEGFGP 91 Query: 317 NMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGS 376 +F VK D R AL+P + +F ++SY++LP++L + S +R+E Sbjct: 92 ELFRVKDRGD-----RPLALRPTSEEVITDMFRKWIRSYKDLPLKLYQIQSKFRDEKRPR 146 Query: 377 LHGLMRVRGFTQDDAHVF-CTKEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRV 435 GL+R R F DA+ F +E K+ + I+ V Sbjct: 147 -FGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSRIFLRLPLIFGPV---------- 195 Query: 436 GSDALWDDAENIMKGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGT 495 D I G Y +FE ++ D G + Q T Sbjct: 196 -----PADEGFI------------------------GGSYSHEFEALMPD--GGEDQIAT 224 Query: 496 IQVDFNLPSRFNAFYVNSHSEKCHP---VMIHRAVFGSIERFIGIMI----ENFKGNLPL 548 + + F +++ E +H +G R IG I +N LP Sbjct: 225 SH---HYGANFEKAFIDIKFEDEEEGELEYVHTTSYGISTRIIGAAILIHGDNEGLVLPP 281 Query: 549 WLSPIQAIVTTITSSA-------VEYAQEIANLLKSHHLSIETDFR-NETINYKIREHSI 600 ++ IQ ++ I V Y +++A L+ + +E D R + +K+ Sbjct: 282 IVADIQVVIVPIFIKGANEHYKVVNYGRDVAEPLEKLGIRVEGDDRSPDGPGFKLNIWEG 341 Query: 601 KKIPIIIICGDKEASERSIGIRR 623 ++ I G K + + + Sbjct: 342 IEVGHIFELGTKYSEAMNATVLD 364 >gnl|CDD|133437 cd01667, TGS_ThrRS_N, TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood. Length = 61 Score = 80.6 bits (200), Expect = 1e-15 Identities = 34/60 (56%), Positives = 43/60 (71%), Gaps = 1/60 (1%) Query: 5 IKLTFPDGSIKNFPVHATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVRE-GSIEIIT 63 IK+T PDGS+K FP T D+A+SIS LAKKAVA +NG++ DLS P+ E +EIIT Sbjct: 1 IKITLPDGSVKEFPKGTTPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDCELEIIT 60 >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 = 77.0 bits (189), Expect = 1e-14 Identities = 58/267 (21%), Positives = 94/267 (35%), Gaps = 63/267 (23%) Query: 275 IFQTLISYMRRKIKD-DYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRT 333 I + +RR + + ++E+ TP V + L +++GH + A D Sbjct: 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDLLPVGAENEED-------- 52 Query: 334 FALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHV 393 L+P PG V +F + R+LP+RLAE G +RNE GL RVR FTQ + V Sbjct: 53 LYLRPTLEPGLVRLFVSHI---RKLPLRLAEIGPAFRNEGGRR--GLRRVREFTQLEGEV 107 Query: 394 FCTKEQMFNECLKIHNLIISIYKD-----FGFEKIMVKLSTRPEKRVGSDALWDDAENIM 448 F E +I + ++ I+ T E G Sbjct: 108 FGEDG----EEASEFEELIELTEELLRALGIKLDIVFVEKTPGEFSPG------------ 151 Query: 449 KGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGTIQVDFNLPSR-FN 507 GP FE + GR + G+ + +R + Sbjct: 152 -------------------------GAGPGFEIEVDHPEGRGLEIGSGGYRQDEQARAAD 186 Query: 508 AFYVNSHSEKCHPVMIHRAVFGSIERF 534 ++++ E +P I +ER Sbjct: 187 LYFLDEALEYRYPPTIGFG--LGLERL 211 >gnl|CDD|73229 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline 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. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.. Length = 255 Score = 69.0 bits (169), Expect = 4e-12 Identities = 48/189 (25%), Positives = 88/189 (46%), Gaps = 11/189 (5%) Query: 240 ESEKRDHRKLAREMDLFHIAEDGSGVIFWHRKGWKIFQTLISYMRRKI-KDDYEEINTPQ 298 ++E H+ L R I + SG+ W G ++ + + + +R ++ K +EI P Sbjct: 1 DAEIISHKLLLR---AGFIRQTSSGLYSWLPLGLRVLKKIENIIREEMNKIGAQEILMPI 57 Query: 299 VLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYREL 358 + LW++SG WD+Y + +K + F L P + + + +KSY++L Sbjct: 58 LQPAELWKESGRWDAYGPELLRLKDRHG-----KEFLLGPTHEEVITDLVANEIKSYKQL 112 Query: 359 PVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFCT-KEQMFNECLKIHNLIISIYKD 417 P+ L + + +R+E GLMR R F DA+ F +E + K++ I+K Sbjct: 113 PLNLYQIQTKFRDEIR-PRFGLMRGREFLMKDAYSFDIDEESLEETYEKMYQAYSRIFKR 171 Query: 418 FGFEKIMVK 426 G + V+ Sbjct: 172 LGLPFVKVE 180 >gnl|CDD|145985 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain. Length = 93 Score = 68.0 bits (167), Expect = 8e-12 Identities = 23/89 (25%), Positives = 44/89 (49%) Query: 556 IVTTITSSAVEYAQEIANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEAS 615 I +YAQ++A L+ + +E D RNE++ K R+ + IP ++ G+KE Sbjct: 5 IPLGEKDELEDYAQKLAEELREAGIRVELDDRNESLGKKFRDADLIGIPFRLVVGEKELE 64 Query: 616 ERSIGIRRFGSTTTQKVSLLDAIPILTKE 644 ++ +R + + VSL + + L + Sbjct: 65 NGTVTVRDRDTGEKETVSLEELVEKLKEL 93 >gnl|CDD|37535 KOG2324, KOG2324, KOG2324, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 457 Score = 59.2 bits (143), Expect = 4e-09 Identities = 70/359 (19%), Positives = 133/359 (37%), Gaps = 60/359 (16%) Query: 293 EINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVF-NHG 351 +I+ P + + LW+++G WD+ + +F + + L P + A+ + Sbjct: 73 KISLPILSSKELWEKTGRWDAMGSELFRLHDRKG-----KQMCLTPTHEEDITALMATYI 127 Query: 352 LKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFCTKE----QMFNECLKI 407 SY++LP+R+ + G +R+E GL+R R F D + F + E Q + + Sbjct: 128 PLSYKQLPIRVYQIGRKFRDELRPRF-GLLRGREFLMKDMYSFDSDEETAQQTYQLVDQA 186 Query: 408 HNLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLD----TIKNSSQDRI 463 ++ I+K G + V + + G + I +D + Sbjct: 187 YD---RIFKQLGLPFVKVWADS----------------GDIGGEVSHEFHLIHPVGEDTL 227 Query: 464 NT----GVLLGEGAFYGPKFEYILKDAIGRDWQCGTIQVD--FNL----PSRFNAFYVNS 513 + G K K GR + +I+V F L NA +VN Sbjct: 228 MSCPSCGYSKNSEDLDLSKIASCPKCNEGRLTKTKSIEVGHTFLLGTKYSKPLNAKFVNV 287 Query: 514 HSEKCHPVMIHRAVFG-SIERFIGIMIENFKGN----LPLWLSPIQAIVTTITSS----- 563 + P +H +G + R + E + P ++P + + Sbjct: 288 EGK---PEFLHMGCYGIGVTRLLAAAAEVLSDDKGLRWPSLIAPYKVCLIGPKKGSKSQR 344 Query: 564 AVEYAQEI--ANLLKSHHLSIETDFRNE-TINYKIREHSIKKIPIIIICGDKEASERSI 619 A E E+ + + H I D R E TI +I++ + IP +I+ G+ + + Sbjct: 345 AQEVISELLNDEAVGNLHGEILLDDREELTIGKRIKDANRLGIPFVIVVGNSASWDNPE 403 >gnl|CDD|145794 pfam02824, TGS, TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 60 Score = 56.0 bits (136), Expect = 3e-08 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%) Query: 5 IKLTFPDGSIKNFPVHATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVREG-SIEIIT 63 I++ PDG + P +T D A +I L KK + +NG+ L + +G +EI+T Sbjct: 1 IRVYTPDGKVPELPRGSTPEDFAYAIHTDLGKKFIGAKVNGQRVGLDHVLEDGDVVEIVT 60 >gnl|CDD|29823 cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline 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. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.. Length = 261 Score = 55.2 bits (133), Expect = 6e-08 Identities = 56/281 (19%), Positives = 112/281 (39%), Gaps = 47/281 (16%) Query: 263 SGVIFWHRKGWKIFQTLISYMRRKIKD-DYEEINTPQVLDQHLWQ-QSGHWDSYRANMFA 320 G + + G+ I++ + + ++IK+ +E + P ++ + + + H + + + Sbjct: 22 KGCMVFRPYGYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKEHIEGFAPEVAW 81 Query: 321 VKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGL 380 V + AL+P + +F+ ++SYR+LP+++ ++ +V+R E + Sbjct: 82 VTHGGLEELEEP-LALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRWETKTT-RPF 139 Query: 381 MRVRGFTQDDAH-VFCTKEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRVGSDA 439 +R R F + H T+E+ E L+I +L Y+D I V + E Sbjct: 140 LRTREFLWQEGHTAHATEEEAEEEVLQILDLYKEFYED--LLAIPVVKGRKTEW------ 191 Query: 440 LWDDAENIMKGVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGTI-QV 498 ++ GA Y E ++ D GR Q GT + Sbjct: 192 ---------------------EKF-------AGADYTYTIEAMMPD--GRALQSGTSHNL 221 Query: 499 DFNLPSRFNAFYVNSHSEKCHPVMIHRAVFGSIERFIGIMI 539 N F+ Y + +K + H+ +G R IG +I Sbjct: 222 GQNFSKAFDIKYQDKDGQKEYV---HQTSWGISTRLIGAII 259 >gnl|CDD|58340 cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline 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 = 264 Score = 54.7 bits (131), Expect = 9e-08 Identities = 34/178 (19%), Positives = 65/178 (36%), Gaps = 3/178 (1%) Query: 262 GSGVIFWHRKGWKIFQTLISYMRRKIKDD-YEEINTPQVLDQHLWQQSGHWDSYRANMFA 320 G G+I + I + + + + K+ + P + ++ D + A Sbjct: 21 GRGIINFLPLAKAILDKIENVLDKMFKEHGAQNALFPFFILASFLEKEAEHDEGFSKELA 80 Query: 321 VKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGL 380 V + FAL+P + +KS+++LP L + G+ +R+E G Sbjct: 81 VFKDAGDEELEEDFALRPTLEENIGEIAAKFIKSWKDLPQHLNQIGNKFRDEIR-PRFGF 139 Query: 381 MRVRGFTQDDAHVF-CTKEQMFNECLKIHNLIISIYKDFGFEKIMVKLSTRPEKRVGS 437 +R R F D H E+ E L + + I +D + + K G+ Sbjct: 140 LRAREFIMKDGHSAHADAEEADEEFLNMLSAYAEIARDLAAIDFIEGEADEGAKFAGA 197 >gnl|CDD|29797 cd00738, HGTP_anticodon, HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).. Length = 94 Score = 52.6 bits (126), Expect = 3e-07 Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 6/92 (6%) Query: 552 PIQAIVTTIT---SSAVEYAQEIANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIII 608 PI + +T A EYAQ++ N L ++ + + D R I K RE ++ +P ++ Sbjct: 1 PIDVAIVPLTDPRVEAREYAQKLLNALLANGIRVLYDDRERKIGKKFREADLRGVPFAVV 60 Query: 609 CGDKEASERSIGIRRFGSTTTQKVSL-LDAIP 639 G+ E + ++ T + +L +D +P Sbjct: 61 VGEDELENGKVTVKS--RDTGESETLHVDELP 90 >gnl|CDD|30473 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 429 Score = 52.5 bits (126), Expect = 3e-07 Identities = 76/440 (17%), Positives = 144/440 (32%), Gaps = 100/440 (22%) Query: 274 KIFQTLISYMRRKIKD-DYEEINTPQVLDQHLWQQSG--HWDSYRANMFAVKCADDTIKD 330 + + + S +R+ + + EI TP L+ + D M+ K D K Sbjct: 19 ALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETDVVEKEMYTFK---D--KG 73 Query: 331 LRTFALKPMNCPGHV-AVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQD 389 R+ AL+P AV + L P++L FG V+R E R R F Q Sbjct: 74 GRSLALRPELTAPVARAVAENKL--DLPKPLKLYYFGPVFRYERPQKG----RYRQFYQF 127 Query: 390 DAHVFCTKEQMFN-ECLKIHNLIISIYKDFGFEKIMVKLSTR--PEKRVGS------DAL 440 V + + E + L + I + G +++++R E R+ +AL Sbjct: 128 GVEVIGSDSPDADAEVIA---LAVEILEALGIGGFTLEINSRGILEGRLEYLGIDQREAL 184 Query: 441 WDDAENIMKGVLDTIKNSSQDRINTGVL-----------------------LGEGAF--- 474 + + K + S+ R+ T L L E + Sbjct: 185 LRYLDKLDKIGKLELDEDSKRRLKTNPLRVLDSKKDSDQELLKNAPELLDYLDEESLEHL 244 Query: 475 ---------YGPKFEYILKDAIGRDWQCGTIQVDFNLPSRFNAFYVNSHSEKCHPVMIHR 525 G +E G D+ GT+ F A ++ Sbjct: 245 EELLALLDALGISYEIDPSLVRGLDYYTGTV---------FEAVTDGLGAQG-------- 287 Query: 526 AVFGS------IERFIG---------------IMIENFKGNLPLWLSPIQAIVTTITSSA 564 +V G +E F G I+ +G + + V + A Sbjct: 288 SVCGGGRYDGLVEEFGGKPTPAVGFAIGVERLILALEEEGKEDPVETRVDVYVVPLGEDA 347 Query: 565 VEYAQEIANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEASERSIGIRRF 624 A ++A L++ +S+E D+ + + + +I G+ E + + ++ Sbjct: 348 EPEALKLAQKLRAAGISVEVDYSGRKLKKQFKYADKLGARFAVILGEDELANGVVTVKDL 407 Query: 625 GSTTTQKVSLLDAIPILTKE 644 + ++V L + + L + Sbjct: 408 ATGEQEEVPLDELVEELKEL 427 >gnl|CDD|29815 cd00770, SerRS_core, Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain 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 in the core domain. SerRS synthetase is a homodimer.. Length = 297 Score = 47.8 bits (114), Expect = 1e-05 Identities = 39/189 (20%), Positives = 80/189 (42%), Gaps = 18/189 (9%) Query: 240 ESEKRDHRKLAREMDL--FHIAEDGSGVIFWHRKGWKIF--QTLISYMRRK-IKDDYEEI 294 + + +DH +L ++D+ F SG F++ KG + LI++ K + + Sbjct: 15 DFKPKDHVELGEKLDILDFERGAKVSGSRFYYLKGDGALLERALINFALDFLTKRGFTPV 74 Query: 295 NTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKS 354 P ++ + + + +G + ++ V + L A P+ A+ + Sbjct: 75 IPPFLVRKEVMEGTGQLPKFDEQLYKV---EGEDLYLIATAEVPLA-----ALHRDEILE 126 Query: 355 YRELPVRLAEFGSVYRNEPSGS----LHGLMRVRGFTQDDAHVFCTKEQMFNECLKIHNL 410 ELP++ A + +R E +GS GL RV F + + VF E+ + E ++ + Sbjct: 127 EEELPLKYAGYSPCFRKE-AGSAGRDTRGLFRVHQFEKVEQFVFTKPEESWEELEELISN 185 Query: 411 IISIYKDFG 419 I ++ G Sbjct: 186 AEEILQELG 194 >gnl|CDD|32699 COG2872, COG2872, Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]. Length = 241 Score = 47.3 bits (112), Expect = 1e-05 Identities = 29/140 (20%), Positives = 56/140 (40%), Gaps = 12/140 (8%) Query: 74 RHSCAHIMAEAVQSIWPEVQVAIGPIIEDGFYYDFDKEQPFSSDELAQIEKKMQEIIARD 133 H+ H+++ + ++ I ED DFD + DE+ ++E E++ + Sbjct: 98 MHTALHLLSAVLYKVYG-ALTTGFEIGEDYARIDFD--GEDTEDEIEEVEALANELVKEN 154 Query: 134 SPFLKQYLSHEKARELFESKKEAYKVEILESIPAKENVTLYRQGEWFDL--CRGPHVRST 191 P + ++ E+A +L K + P E + D+ C G HV++T Sbjct: 155 LPVIIYFIPREEAEKLPGLVKLK-----NKVPPDVEGKIRIVEIGDIDVQPCGGTHVKNT 209 Query: 192 GQVKKFF--KLMKVAGAYWR 209 G++ + K K R Sbjct: 210 GEIGEIKILKTEKKGKGNRR 229 >gnl|CDD|30363 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 879 Score = 46.8 bits (111), Expect = 2e-05 Identities = 34/148 (22%), Positives = 67/148 (45%), Gaps = 21/148 (14%) Query: 65 EDPRSLAVIRHSCAHIMAEAVQSIW-PEVQVAIGPIIEDGFYYDFDKEQPFSSDELAQIE 123 E+ R + H+ H++ A++ + V A + + +DF + +++EL +IE Sbjct: 557 EERRRRLMRNHTATHLLHAALRKVLGDHVWQAGSLVDPEKLRFDFSHYKALTAEELKEIE 616 Query: 124 KKMQEIIARDSPFLKQYLSHEKARE-----LFESKKEAYKVEILESIPAKENVTLYRQGE 178 + + EII + P + + ++A+ LF E Y + V + G+ Sbjct: 617 RLVNEIIRENLPVKTEEMDLDEAKAKGAMALFG---EKY----------GDEVRVVEIGD 663 Query: 179 W-FDLCRGPHVRSTGQVKKFFKLMKVAG 205 + +LC G HV +TG + FK++ G Sbjct: 664 FSVELCGGTHVSNTGDI-GLFKIISEEG 690 >gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 895 Score = 46.1 bits (109), Expect = 3e-05 Identities = 29/159 (18%), Positives = 66/159 (41%), Gaps = 18/159 (11%) Query: 47 VCDLSDPVREG-SIEIITPEDPRSLAVIRHSCAHIMAEAVQSIWPEVQVAIGPIIEDGFY 105 + L + G +E+ E+ R L + H+ H++ A++ + + D Sbjct: 542 IGVLEGDLSVGDQVELHVDEERRQLIMRNHTATHLLNFALRQVLKGTDQKGSLVAPDKLR 601 Query: 106 YDFDKEQPFSSDELAQIEKKMQEIIARDSPFLKQYLSHEKARELFESKKEAYKVEILESI 165 +DF + + ++L ++E K+ E I +++P + L +A+ K+ L ++ Sbjct: 602 FDFSTKGALTKEQLKKVEDKINEFIQKNAPVYAKELPLAEAK----------KIPGLRAV 651 Query: 166 PAK---ENVTLYRQGEW----FDLCRGPHVRSTGQVKKF 197 + + V + G + C G H+ +T + F Sbjct: 652 FDEVYPDPVRVVSVGAGQLTSVEFCGGTHLTNTSHIGDF 690 >gnl|CDD|30521 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 429 Score = 46.0 bits (109), Expect = 3e-05 Identities = 38/198 (19%), Positives = 77/198 (38%), Gaps = 16/198 (8%) Query: 240 ESEKRDHRKLAREMDL--FHIAEDGSGVIFWHRKGW--KIFQTLISYM-RRKIKDDYEEI 294 + E +DH +L ++ L F A SG F+ KG ++ + LI +M K + E+ Sbjct: 137 DFEPKDHVELGEKLGLLDFERAAKVSGSRFYFYKGKGARLERALIQFMLDLHTKHGFTEV 196 Query: 295 NTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKS 354 P +++ +G + +++ V D L P + + Sbjct: 197 LPPYLVNLESMFGTGQLPKFEEDLYKV-EDPD-------LYLIPTAEVPLTNLHRDEILD 248 Query: 355 YRELPVRLAEFGSVYRNEPSGS---LHGLMRVRGFTQDDAHVFCTKEQMFNECLKIHNLI 411 +LP++ + +R+E + GL+RV F + + V E+ E ++ Sbjct: 249 EEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKPEESEEELEEMLGNA 308 Query: 412 ISIYKDFGFEKIMVKLST 429 + ++ +V L T Sbjct: 309 EEVLQELELPYRVVNLCT 326 >gnl|CDD|133438 cd01668, TGS_RelA_SpoT, TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown. Length = 60 Score = 42.9 bits (102), Expect = 3e-04 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%) Query: 10 PDGSIKNFPVHATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVREG-SIEIIT 63 P G I P AT D A +I + + V +NGK+ LS +++G +EIIT Sbjct: 6 PKGEIIELPAGATVLDFAYAIHTEIGNRCVGAKVNGKLVPLSTVLKDGDIVEIIT 60 >gnl|CDD|73226 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine 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. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.. Length = 261 Score = 42.1 bits (99), Expect = 4e-04 Identities = 35/166 (21%), Positives = 55/166 (33%), Gaps = 34/166 (20%) Query: 274 KIFQTLISYMRRKIKDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDL-- 331 I TL R YEEI+TP +F K D+ K++ Sbjct: 7 YIEDTLREVFERY---GYEEIDTPVF--------------EYTELFLRKSGDEVSKEMYR 49 Query: 332 ------RTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRG 385 R AL+P LP++L G V+R E R R Sbjct: 50 FKDKGGRDLALRPDLTAPVARAVAEN-LLSLPLPLKLYYIGPVFRYERPQKG----RYRE 104 Query: 386 FTQDDAHVFCTKEQMFN-ECLKIHNLIISIYKDFGFEKIMVKLSTR 430 F Q + + + + E + L + I + G + +K++ R Sbjct: 105 FYQVGVEIIGSDSPLADAEVIA---LAVEILEALGLKDFQIKINHR 147 >gnl|CDD|39365 KOG4163, KOG4163, KOG4163, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 551 Score = 39.6 bits (92), Expect = 0.003 Identities = 60/291 (20%), Positives = 109/291 (37%), Gaps = 60/291 (20%) Query: 352 LKSYRELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAH-VFCTKEQMFNECLKIHNL 410 ++S+R+LP++L ++ +V R E +R R F + H F T E+ E L+I +L Sbjct: 178 IQSHRDLPLKLNQWCNVVRWEFKHPQ-PFLRTREFLWQEGHTAFATPEEAEEEVLQILDL 236 Query: 411 IISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLDTIKNSSQDRINTGVLLG 470 +Y++ ++ + EK G D T++ Sbjct: 237 YARVYEELLAIPVVKGRKSEKEKFAGGD------------YTTTVE-------------- 270 Query: 471 EGAFYGPKFEYILKDAIGRDWQCGTIQVDFNLPSRFN-AFYVNSHSEKCHP-VMIHRAVF 528 AF GR Q T +L F+ F + + + + Sbjct: 271 --AFIP---------CSGRGIQGAT---SHHLGQNFSKMFEIVFEDPGEGEKEFVWQNSW 316 Query: 529 GSIERFIGIMIENFKGN----LPLWLSPIQAIVTTI----------TSSAVEYAQEIANL 574 G R IG+MI + LP ++P+Q +V + ++ + + Sbjct: 317 GLSTRTIGVMIMTHGDDKGLVLPPRVAPVQVVVVPVGITDATSEEDKQELLDACSAVESR 376 Query: 575 LKSHHLSIETDFR-NETINYKIREHSIKKIPIIIICGDKE-ASERSIGIRR 623 L + E D R N T +K +K +P+ I G ++ AS + + +RR Sbjct: 377 LLGAGIRAEADLRDNYTPGWKFNHWELKGVPLRIEIGPRDLASNQVVAVRR 427 >gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 60 Score = 38.5 bits (90), Expect = 0.006 Identities = 19/53 (35%), Positives = 26/53 (49%) Query: 10 PDGSIKNFPVHATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVREGSIEII 62 PDGS P AT D A I L K + +NG++ DLS +++G I Sbjct: 6 PDGSAVELPKGATAMDFALKIHTDLGKGFIGALVNGQLVDLSYTLQDGDTVSI 58 >gnl|CDD|29801 cd00861, ProRS_anticodon_short, ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.. Length = 94 Score = 37.5 bits (87), Expect = 0.013 Identities = 18/79 (22%), Positives = 38/79 (48%) Query: 564 AVEYAQEIANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEASERSIGIRR 623 E A+++ L++ + + D RNE K + + IP I+ G K A+E + I+ Sbjct: 16 QQELAEKLYAELQAAGVDVLLDDRNERPGVKFADADLIGIPYRIVVGKKSAAEGIVEIKV 75 Query: 624 FGSTTTQKVSLLDAIPILT 642 + +++S+ + + L Sbjct: 76 RKTGEKEEISIDELLEFLQ 94 >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 = 37.1 bits (86), Expect = 0.014 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 7/79 (8%) Query: 356 RELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFC---TKEQMFNECLKIHNLII 412 R+LP +A+ G +RNE S +GL RVR FTQ + F F+ + + Sbjct: 104 RKLPFGVAQIGKSFRNEIS-PRNGLFRVREFTQAEIEFFVDPEKSHPWFDYWA---DQRL 159 Query: 413 SIYKDFGFEKIMVKLSTRP 431 F ++L+ Sbjct: 160 KWLPKFAQSPENLRLTDHE 178 >gnl|CDD|30772 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 558 Score = 37.2 bits (86), Expect = 0.015 Identities = 38/175 (21%), Positives = 59/175 (33%), Gaps = 63/175 (36%) Query: 288 KDDYEEINTPQVLDQHLWQQSGHWDSYRANMFAVKC--------ADDTIKDL-------- 331 ++D EI+TP +L + +W+ SGH D + + V+C AD I++ Sbjct: 58 REDVVEIDTPIILPEEVWKASGHVDKFSDPL--VECKKCGERYRADHLIEEYLGKDGHGN 115 Query: 332 -------RTFALKPMNCP------GHVAVFN----------HGLKSY------------- 355 + CP V FN Y Sbjct: 116 MSPEELTEIIREYDIRCPECGGELNEVREFNLMFKTTIGPVEDSLGYLRPETAQGIFVNF 175 Query: 356 --------RELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFCTKEQMFN 402 +LP +A+ G +RNE S +GL R R F Q + F E+ + Sbjct: 176 KNLLEFARNKLPFGIAQIGKSFRNEISPR-NGLFRTREFEQAEIEFFVDPEEKEH 229 >gnl|CDD|37509 KOG2298, KOG2298, KOG2298, Glycyl-tRNA synthetase and related class II tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 599 Score = 34.9 bits (80), Expect = 0.073 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%) Query: 356 RELPVRLAEFGSVYRNEPSGSLHGLMRVRGFTQDDAHVFC 395 +LP A+ G +RNE S GL+RVR FT + F Sbjct: 206 GKLPFASAQIGKSFRNEIS-PRSGLLRVREFTMAEIEHFV 244 >gnl|CDD|30665 COG0317, SpoT, Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]. Length = 701 Score = 34.1 bits (78), Expect = 0.13 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%) Query: 10 PDGSIKNFPVHATGSDVAESISRSLAKKAVAVAINGKVCDLSDPVREG-SIEIITPEDPR 68 P G + + P AT D A ++ + + + +NG++ L+ ++ G +EIIT + Sbjct: 394 PKGKVIDLPKGATPLDFAYAVHTDIGHRCIGAKVNGRIVPLTTKLQTGDQVEIITSKHAG 453 >gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional. Length = 430 Score = 32.2 bits (73), Expect = 0.41 Identities = 27/117 (23%), Positives = 45/117 (38%), Gaps = 7/117 (5%) Query: 531 IERFIGIMIENFKGNLPLWLSPIQAIVTTITSSAVEYAQEIANLLKSHHLSIETDFRNET 590 +ER + I K N+ L I + T A + EI L+ ++ E D + Sbjct: 308 LERLLLIA----KDNIILPKQSIDVYIATQGLKAQKKGWEIIQFLEKQNIKFELDLSSSN 363 Query: 591 INYKIREHSIKKIPIIIICGDKEASERSIGIRRFGST---TTQKVSLLDAIPILTKE 644 + +I++ K+ II GD E + I I+ Q + I L K+ Sbjct: 364 FHKQIKQAGKKRAKACIILGDNEIMDNCITIKWLDEQVQENAQYSNFKQEISYLKKK 420 >gnl|CDD|37720 KOG2509, KOG2509, KOG2509, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 455 Score = 31.4 bits (71), Expect = 0.78 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 13/69 (18%) Query: 356 RELPVRLAEFGSVYRNEPSGSLH---GLMRVRGFTQDDAHVFCTKEQ---MFNECLKIHN 409 +LP++ +R E GL RV F + + V E M E Sbjct: 263 DQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSWEMLEE------ 316 Query: 410 LIISIYKDF 418 +I+ ++F Sbjct: 317 -MINNQEEF 324 >gnl|CDD|145636 pfam02597, ThiS, ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end. Length = 70 Score = 31.1 bits (71), Expect = 1.0 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 5/51 (9%) Query: 19 VHATGSDVAESISR-SLAKKAVAVAINGKVCDLSD---PVREGS-IEIITP 64 G+ VAE + L + VAVA+NG++ S P+++G + II P Sbjct: 16 ELPEGATVAELLEALGLNPERVAVAVNGEIVPRSQADTPLKDGDEVAIIPP 66 >gnl|CDD|176353 cd00565, ThiS, ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity. Length = 65 Score = 31.0 bits (71), Expect = 1.1 Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 5/37 (13%) Query: 33 SLAKKAVAVAINGKVCDLSD----PVREG-SIEIITP 64 L + VAVA+NG++ S+ P+++G IEI+T Sbjct: 25 GLDPRGVAVALNGEIVPRSEWASTPLQDGDRIEIVTA 61 >gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 577 Score = 29.8 bits (67), Expect = 2.3 Identities = 10/99 (10%), Positives = 30/99 (30%), Gaps = 18/99 (18%) Query: 234 YLYFLEESEKRDHRKLAREMDLFHIAEDGSGVIFWHRKGWKIFQTLISYMRRKIKDDYEE 293 Y+ ++ E+ + E G + ++++ + IK+ + Sbjct: 199 YVKIAKDLEEDPGNDEEEAREEVEKLESG-------DEEAELWRKFVDLSLEGIKETLDR 251 Query: 294 INTPQVLDQHLWQQSGHWDSYRANMFAVKCADDTIKDLR 332 + D + + S+ + ++DL Sbjct: 252 LGVK--FDVYDSEGE----SFYNGKV-----EKVVEDLE 279 >gnl|CDD|36737 KOG1524, KOG1524, KOG1524, WD40 repeat-containing protein CHE-2 [General function prediction only]. Length = 737 Score = 29.2 bits (65), Expect = 3.5 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%) Query: 406 KIHNLIISIYKDFGFEKIMVKLSTRPEKRVGSDALWDDAENIMKGVLDT 454 K +L I+ K FG E+ + K+ T W+D NI+ G+ DT Sbjct: 472 KNRDLFITSVKRFGKEEEIYKIGTMVHTLA-----WNDTTNILCGLQDT 515 >gnl|CDD|38910 KOG3706, KOG3706, KOG3706, Uncharacterized conserved protein [Function unknown]. Length = 629 Score = 29.2 bits (65), Expect = 4.0 Identities = 26/144 (18%), Positives = 43/144 (29%), Gaps = 17/144 (11%) Query: 324 ADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFG--SVYRNEPSGSLHGLM 381 D KD AL P + G R V +F +V R + Sbjct: 492 VDQMAKDFIHHALPPYLTGDEAELSVPGGALERLNSVVRLQFTDHTVVRLLRDQIQRLVT 551 Query: 382 RVRG-----FTQDDAHVFCTKEQMFNECL----KIHNLIISIYKDFGFEKIMVKLSTRPE 432 G + ++ + E+ E L L+ Y +KL++ E Sbjct: 552 ESEGMVFIYHSVKNSREYHMMEETEFEILPFPADALELLKQSYNPEAISVKDLKLTSDEE 611 Query: 433 KRVGSDALWDDAENIMKGVLDTIK 456 K + +LW +G+L Sbjct: 612 KLSLATSLWT------EGLLLVKN 629 >gnl|CDD|38949 KOG3745, KOG3745, KOG3745, Exocyst subunit - Sec10p [Intracellular trafficking, secretion, and vesicular transport]. Length = 763 Score = 28.7 bits (64), Expect = 5.3 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%) Query: 108 FDKEQPFSSDELAQIEKKMQEIIARDSPFLKQYLSHEKA------RELFESKKEAYKVEI 161 F EQPF S+ L I + ++ +S F+K+ + + + +F K + E+ Sbjct: 258 FQPEQPFISNILQDIFNDILKLCESESKFIKRVFPNPETVLQKFIQNIFGQKIKDRVEEL 317 Query: 162 LESIPAKENVTLY 174 LE ++ Y Sbjct: 318 LEECKEGKDFLAY 330 >gnl|CDD|80310 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41.. Length = 232 Score = 28.7 bits (64), Expect = 5.6 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%) Query: 389 DDAHVFCTKEQMFNECLK-----IHNLIISIYKDFGFEKIMVKLSTR 430 DD C+ + +C K + L + +DFGF+ I+ S R Sbjct: 90 DDVRTCCSGATICEKCWKFAKEAVKILDDILREDFGFKHILWVFSGR 136 >gnl|CDD|32399 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and metabolism]. Length = 713 Score = 28.3 bits (63), Expect = 7.4 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%) Query: 36 KKAVAVAINGKVCD---LSDPVREGSIEII 62 K V VA++GK+ L+D +R + E I Sbjct: 517 KTVVFVAVDGKLVGVIALADELRPDAKEAI 546 >gnl|CDD|37859 KOG2648, KOG2648, KOG2648, Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]. Length = 453 Score = 28.0 bits (62), Expect = 8.4 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 3/57 (5%) Query: 527 VFGSIERFIGIMIENFKGNLPLWLSPIQAIVTTITSSAVEYAQEIANLLKSHHLSIE 583 VF I + ++++ + N P I IV T + +A LK L +E Sbjct: 126 VFVDIPIDLDHLVKSLQRNFP---QLISQIVLLGTIQFAHSLEALATELKEELLDLE 179 >gnl|CDD|73265 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.. Length = 143 Score = 28.0 bits (62), Expect = 9.1 Identities = 8/49 (16%), Positives = 18/49 (36%) Query: 571 IANLLKSHHLSIETDFRNETINYKIREHSIKKIPIIIICGDKEASERSI 619 A L + + E I+ + + + ++I D A R++ Sbjct: 58 AARRLNELNPGVNVTAVPEGISEDNLDDFLDGVDLVIDAIDNIAVRRAL 106 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 0.321 0.136 0.412 Gapped Lambda K H 0.267 0.0786 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,157,735 Number of extensions: 444978 Number of successful extensions: 1189 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1150 Number of HSP's successfully gapped: 54 Length of query: 652 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 552 Effective length of database: 4,102,837 Effective search space: 2264766024 Effective search space used: 2264766024 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: 61 (27.2 bits)