RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780949|ref|YP_003065362.1| tyrosyl-tRNA synthetase [Candidatus Liberibacter asiaticus str. psy62] (418 letters) >gnl|CDD|30511 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 401 Score = 399 bits (1027), Expect = e-112 Identities = 182/410 (44%), Positives = 243/410 (59%), Gaps = 17/410 (4%) Query: 5 KSDFLSILSERGFIHQISNPRELDILCSQGVVTAYIGYDLTASSLHAGHLTQLMLLFWLQ 64 L L +RG I QI++ EL L +G + YIG+D TA SLH GHL LM L Q Sbjct: 2 MDVELLELIKRGLIEQITDEEELRKLLEEGPLRVYIGFDPTAPSLHLGHLVPLMKLRRFQ 61 Query: 65 KTGHKPISLMGGGTSIIGDPSFRDESRRMMRSQEIQENIEKIKGIFSSFIKYGTGKTDAL 124 GHKPI L+G T++IGDPS + E R+++ + + EN E IK F+ A Sbjct: 62 DAGHKPIVLIGDATAMIGDPSGKSEERKLLTRETVLENAETIKKQLGKFLD-----NKAE 116 Query: 125 MLNNETWLCSIKYIDLLREIGSFFSVNRMLSFESVRSRLKREQSLSFLEFNYMILQAYDF 184 +NN WL + Y+D LR++G FSVNRML + V+ RL+REQ +SF EFNY +LQAYDF Sbjct: 117 FVNNSDWLKKLNYLDFLRDVGKHFSVNRMLRRDDVKKRLEREQGISFTEFNYPLLQAYDF 176 Query: 185 VELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPKLFALTSPLLTTASGTKMGKTLSGA 244 V L K+ LQ+GGSDQWGNI+ G DL RL K+ LT+PLLT G KMGK+ GA Sbjct: 177 VYLNKD----LQLGGSDQWGNILAGRDLIRRLGQKKVVGLTTPLLTGLDGKKMGKSEGGA 232 Query: 245 IWLNKEMTSPYNFWQYWRNIDDADVVSFAKRLTTLPMSEIDRMAK--LQGKEINEAKKII 302 +WL+ E TSPY+F+QYW NI+DADV F K LT L + EI+ + K L+G E EAKK++ Sbjct: 233 VWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLEEIEEIEKYVLKGPEPREAKKLL 292 Query: 303 ATEITTMVHGREEAEKAATAAMECFDMSIHSQHMPTISISKDEVSRGMGLLTLIVKAGFA 362 A E+T +VHG E AE A + F + ++P + + GL+ L+V AG A Sbjct: 293 AKEVTKLVHGEEAAEAAEEEFEKLFSEGLPE-NLPPADLKQ---KLEDGLVDLLVDAGLA 348 Query: 363 TSTNEARRHLKSNAIKINNSIISNEKLQIKLQDFDSTGNIKLSFGKKNHI 412 S +EARR ++ +KIN + +E + D G + L GKK Sbjct: 349 PSRSEARRLIQQGGVKINGEKVEDENYVL--SDLLDNGLLVLRRGKKKFA 396 >gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. Length = 269 Score = 300 bits (770), Expect = 6e-82 Identities = 115/276 (41%), Positives = 162/276 (58%), Gaps = 9/276 (3%) Query: 36 VTAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESRRMMR 95 + YIG+D TA SLH GHL LM L Q+ GH+ I L+G T++IGDPS + E R+++ Sbjct: 1 LKVYIGFDPTAPSLHLGHLVPLMKLRDFQQAGHEVIVLIGDATAMIGDPSGKSEERKLLD 60 Query: 96 SQEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLS 155 + I+EN + K + + + A +NN WL S+ +D LR +G F+VNRML Sbjct: 61 LELIRENAKYYKKQLKAILDFI-PPEKAKFVNNSDWLLSLYTLDFLR-LGKHFTVNRMLR 118 Query: 156 FESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGER 215 ++V+ RL+ E+ +SF EF Y +LQAYDFV L LQ+GGSDQ GNI G DL + Sbjct: 119 RDAVKVRLEEEEGISFSEFIYPLLQAYDFVYLDV----DLQLGGSDQRGNITLGRDLIRK 174 Query: 216 LKTPKLFALTSPLLTTASGTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKR 275 L K+ LT+PLLT G KM K+ AIW + + SPY+ +Q RN D DV+ F K Sbjct: 175 LGYKKVVGLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKL 233 Query: 276 LTTLPMSEIDRMAKLQGKEI--NEAKKIIATEITTM 309 T L EI+ + + + +AKK +A E+T + Sbjct: 234 FTFLDYEEIEELEEEHAEGPLPRDAKKALAEELTKL 269 >gnl|CDD|37834 KOG2623, KOG2623, KOG2623, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 467 Score = 298 bits (764), Expect = 2e-81 Identities = 152/433 (35%), Positives = 233/433 (53%), Gaps = 26/433 (6%) Query: 7 DFLSILSERGFIHQI---SNPRELDILCSQGV-VTAYIGYDLTASSLHAGHLTQLMLLFW 62 D+L+ L RG + + + L +G+ Y G+D TA SLH G+L LM+L Sbjct: 31 DYLTELKARGLFQTSFPETLSKCSEDLNGRGLPQYVYCGFDPTAESLHVGNLLALMVLIH 90 Query: 63 LQKTGHKPISLMGGGTSIIGDPSFRDESRRMMRSQEIQENIEKI----KGIFSS---FIK 115 Q+ GH+PI+L+GG T+ +GDPS R R + + N I IF + + + Sbjct: 91 FQRAGHRPIALIGGATASVGDPSGRKTERGQLAEDTREANSRSITQQLCKIFENHPEYYR 150 Query: 116 YGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLSFESVRSRLKREQSLSFLEFN 175 G+ + +++NN W IK +D L E+G F V ML+ +SV+SRL+ LSF EF Sbjct: 151 DGSSQGKYIIVNNSDWYKDIKLLDFLAEVGRHFRVGSMLARDSVKSRLESPNGLSFTEFT 210 Query: 176 YMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPK--LFALTSPLLTTAS 233 Y +LQAYDF L +NY CR Q+GGSDQWGNI G DL ++ + +F LT PLLT+++ Sbjct: 211 YQLLQAYDFYHLYENYGCRFQLGGSDQWGNITAGTDLIRKIMPIQAFVFGLTFPLLTSST 270 Query: 234 GTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKRLTTLPMSEIDRMAKLQGK 293 G K+GK+ A+WL+ TSPY+ +Q++ ++ D DV F K T LP+ EI ++ + K Sbjct: 271 GAKLGKSAGNAVWLDPSKTSPYHLYQFFASLPDDDVEKFLKLFTFLPLEEIKQILEEHRK 330 Query: 294 EI--NEAKKIIATEITTMVHGRE---EAEKAATA-------AMECFDMSIHSQHMPTISI 341 E A+K++A E+T MVHG+E AE+ A + +S Q + Sbjct: 331 EPSQRIAQKLLAAEVTRMVHGKEGLEVAERCTKALFGAKKAGLSGLSLSEILQLFKDATF 390 Query: 342 SKDEVSRGMGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQDFDSTGN 401 + G+ +L L+ KA S EARR ++ + +N+ + +E + I + Sbjct: 391 IDLKDEPGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSIAGPFILNNRG 450 Query: 402 IK-LSFGKKNHII 413 + L GK+N +I Sbjct: 451 LSLLRAGKRNFVI 463 >gnl|CDD|173893 cd00395, Tyr_Trp_RS_core, catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. Length = 273 Score = 230 bits (588), Expect = 4e-61 Identities = 110/274 (40%), Positives = 148/274 (54%), Gaps = 6/274 (2%) Query: 37 TAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESRRMMRS 96 T Y G D TA SLH GHL L+ Q GH+PI L+GG T IIGDPS + R + Sbjct: 1 TLYCGIDPTADSLHIGHLIGLLTFRRFQHAGHRPIFLIGGQTGIIGDPSGKKSERTLNDP 60 Query: 97 QEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLSF 156 +E+++NI +I + + + T A + NN W + +I LR++G VN M Sbjct: 61 EEVRQNIRRIAAQYLAVGIFEDP-TQATLFNNSDWPGPLAHIQFLRDLGKHVYVNYMERK 119 Query: 157 ESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERL 216 S +SR E+ +S EF Y LQA DF+ L C +Q GGSDQWGNI G +L R Sbjct: 120 TSFQSRS--EEGISATEFTYPPLQAADFLLLNTTEGCDIQPGGSDQWGNITLGRELARRF 177 Query: 217 K-TPKLFALTSPLLTTASGTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKR 275 LT PL+T G K GK+ SG WL+ E TSPY F+Q+W N D+DV++ K Sbjct: 178 NGFTIAEGLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKY 237 Query: 276 LTTLPMSEIDRMAKLQ--GKEINEAKKIIATEIT 307 T L EI+R+ + Q A+K +A E+T Sbjct: 238 FTFLSKEEIERLEQEQYEAPGYRVAQKTLAEEVT 271 >gnl|CDD|144245 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y). Length = 291 Score = 229 bits (586), Expect = 1e-60 Identities = 109/302 (36%), Positives = 156/302 (51%), Gaps = 19/302 (6%) Query: 32 SQGVVTAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESR 91 + + Y G+D T LH G+L LM L Q+ GH+ L+G T+IIGDPS + E R Sbjct: 2 KERPLRVYTGFDPTGP-LHLGYLVPLMKLVQFQQAGHEVFFLIGDLTAIIGDPS-KSEER 59 Query: 92 RMMRSQEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVN 151 +++ +E+ EN + K + ++NN WL ++ LLR++G+ FS+N Sbjct: 60 KLLSREEVLENAKAQLACGLDPEK-------SEIVNNSDWLEHLELAWLLRDLGNHFSLN 112 Query: 152 RMLSFESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGID 211 RML F+ V+ RLK+ +S EF Y +LQA D + L + LQ GGSDQWG+I G D Sbjct: 113 RMLQFKDVKKRLKQNPGISLGEFTYPLLQAADILLLKAD----LQPGGSDQWGHIELGRD 168 Query: 212 LGERLKT---PKLFALTSPLLTTASGT-KMGKTLSG-AIWLNKEMTSPYNFWQYWRNIDD 266 L R K LT+PLLT G KM K+ AI+L+ E S Y Q D Sbjct: 169 LARRFNKKVFKKPVGLTNPLLTGLDGGKKMSKSAGNSAIFLDDEKESVYKKIQKAYTDPD 228 Query: 267 ADVVSFAKRLTTLPMSEIDRMAKLQGK-EINEAKKIIATEITTMVHGREEAEKAATAAME 325 +V K T L EI+ + GK EA++++A E+T +VHG + + AA A Sbjct: 229 REVRKDLKLFTELSNEEIEILEAFLGKGPKREAEELLAREVTGLVHGGDLKKAAAEAVNA 288 Query: 326 CF 327 Sbjct: 289 LL 290 >gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Length = 143 Score = 52.5 bits (126), Expect = 2e-07 Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%) Query: 173 EFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPK-LFALTSPLLTT 231 + YM LQA DF+ L + C + +GGSDQ G+I G++L ++ P F LT + Sbjct: 75 DVEYMFLQAADFLLLYETE-CDIHLGGSDQLGHIELGLELLKKAGGPARPFGLTFGRVMG 133 Query: 232 ASGTKMGKTL 241 A GTKM K+ Sbjct: 134 ADGTKMSKSK 143 >gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.. Length = 70 Score = 40.6 bits (95), Expect = 9e-04 Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%) Query: 350 MGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQD---FDSTGNIKLSF 406 M L ++ + G A S +EAR+ +K + +N +++ ++K D D + Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIV 60 Query: 407 GKKNHII 413 + ++ Sbjct: 61 YEDKKLL 67 >gnl|CDD|144902 pfam01479, S4, S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Length = 48 Score = 39.0 bits (92), Expect = 0.002 Identities = 11/46 (23%), Positives = 27/46 (58%) Query: 350 MGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQD 395 M L ++ + G A+S +EAR+ ++ +++N ++ + ++K D Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGD 46 >gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 386 Score = 29.5 bits (66), Expect = 2.0 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 19/114 (16%) Query: 216 LKTPKLFA---LTSP----LLTTASGTKMGKTL--------SGAIWLNKEMTSPYNFWQY 260 L+ P+LFA L P LL GT GKT+ +GA ++N +++ + W Sbjct: 112 LRRPELFAKGKLLRPPKGILLYGPPGT--GKTMLAKAIAKEAGANFINVSVSNLTSKWFG 169 Query: 261 WRNIDDADVVSFAKRL--TTLPMSEIDRMAKLQGKEINEAKKIIATEITTMVHG 312 V S A +L + + + E+D + +EA ++ E + G Sbjct: 170 EAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDG 223 >gnl|CDD|37356 KOG2145, KOG2145, KOG2145, Cytoplasmic tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 397 Score = 28.0 bits (62), Expect = 5.1 Identities = 11/33 (33%), Positives = 16/33 (48%) Query: 39 YIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPI 71 Y G ++ S+H GHL + WLQ P+ Sbjct: 89 YTGRGPSSESMHLGHLIPFIFTKWLQDVFDVPL 121 >gnl|CDD|36810 KOG1597, KOG1597, KOG1597, Transcription initiation factor TFIIB [Transcription]. Length = 308 Score = 27.6 bits (61), Expect = 7.6 Identities = 10/30 (33%), Positives = 14/30 (46%) Query: 281 MSEIDRMAKLQGKEINEAKKIIATEITTMV 310 EI +A + KEI K+I + T V Sbjct: 167 FKEISAVANVSKKEIGRCVKLIGEALETSV 196 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.320 0.134 0.392 Gapped Lambda K H 0.267 0.0690 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,879,614 Number of extensions: 252052 Number of successful extensions: 683 Number of sequences better than 10.0: 1 Number of HSP's gapped: 660 Number of HSP's successfully gapped: 15 Length of query: 418 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 322 Effective length of database: 4,189,273 Effective search space: 1348945906 Effective search space used: 1348945906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (26.6 bits)