RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780573|ref|YP_003064986.1| cysteinyl-tRNA synthetase
[Candidatus Liberibacter asiaticus str. psy62]
         (461 letters)



>gnl|CDD|30564 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 464

 Score =  523 bits (1348), Expect = e-149
 Identities = 212/485 (43%), Positives = 283/485 (58%), Gaps = 49/485 (10%)

Query: 4   KIKIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGE 63
            +K+YNTL R+  EF  IDP  ++MYVCGPTVYD+AHIG+AR  +VFDVL R LRY   +
Sbjct: 1   MLKLYNTLTRQKEEFVPIDPGKVKMYVCGPTVYDYAHIGHARTYVVFDVLRRYLRYLGYK 60

Query: 64  KCVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQP 123
             VTYVRNITDIDDKII RAR+E  SI        +  +    F +D   L  L P  +P
Sbjct: 61  --VTYVRNITDIDDKIINRAREEGLSI------REVAERYIAAFFEDMDALNVLPPDIEP 112

Query: 124 RATNHIPQMIYLIQNIILHGHAYEA-NNEIIFDTSSIPNYGSFSRR-KIDEQKMGTRVPE 181
           RAT HI ++I  I+ +I  G+AY A + ++ FD S   +YG  S R  ++E + G RV  
Sbjct: 113 RATEHIDEIIEFIEKLIEKGYAYVADDGDVYFDVSKFKDYGKLSGRDSLEELQAGARVEV 172

Query: 182 KYHKKNPADFILWKRSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLDLI 241
              K+NP DF+LWK + P EP W+SPWG+GRPGWHIECSAMS+ YLG+ FDIHGGG DLI
Sbjct: 173 DEEKRNPLDFVLWKAAKPGEPSWDSPWGKGRPGWHIECSAMSTKYLGETFDIHGGGSDLI 232

Query: 242 FPHHENEIAQSCCADRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRS 301
           FPHHENEIAQS  A  ++  A  W+HNGFLN++G KMSKS GNFIT+ +LL+        
Sbjct: 233 FPHHENEIAQSEAATGVKPFAKYWMHNGFLNIDGEKMSKSLGNFITVRDLLKK------- 285

Query: 302 WPAPVIRLAMLMTHYREPIDFTVQRLTEAEILLSKWPQT---------STSKGIIDP--- 349
           +   V+RL +L +HYR P+DF+ + L EA+  L +                   +     
Sbjct: 286 YDPEVLRLFLLSSHYRSPLDFSEELLEEAKKALERLYNALRRLRDLAGDAELADLKEFEA 345

Query: 350 AVLSALYNDLNTVSAIQALHKLARESTKNHD--------LLPIFNASAHILGIEVCKEHL 401
               AL +D NT  A+  L +LA+E  +  +        +L    A   ILG++V     
Sbjct: 346 RFREALDDDFNTPKALAVLFELAKEINRLLEEGKSDAKAVLSALKALLAILGLKVLGLFP 405

Query: 402 N------KNISIAIEKLVQERLILLKMKKFSSADYIRKQLESKGFILEDYKNPDNGQRMT 455
                  ++    IE L++ERL   K K ++ AD IR +L + G ILED  +       T
Sbjct: 406 QSGAQEDESDDEEIEALIEERLEARKAKNWALADEIRDELLALGIILEDTPDG------T 459

Query: 456 RWKQK 460
            W++K
Sbjct: 460 TWRRK 464


>gnl|CDD|37218 KOG2007, KOG2007, KOG2007, Cysteinyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 586

 Score =  373 bits (958), Expect = e-104
 Identities = 178/497 (35%), Positives = 251/497 (50%), Gaps = 59/497 (11%)

Query: 1   MKKKIKIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYY 60
              ++K+YN+L R+   F   + + +  Y+CGPTVYD +H+G+AR  + FD+L R+LR Y
Sbjct: 31  QPTELKLYNSLTRQKEVFIPNNGNKVTWYICGPTVYDSSHMGHARSYVSFDILRRILRDY 90

Query: 61  YGEKCVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPT 120
           +G   VT+V NITD+DDKII+RAR+E         +S       ++F++D   L  L PT
Sbjct: 91  FGYD-VTFVMNITDVDDKIIKRARKEEMGEKPLS-LSERFCYYEEEFLQDMAALNVLPPT 148

Query: 121 HQPRATNHIPQMIYLIQNIILHGHAYEANNEIIFDTSSIP-NYGSFSRRKIDEQKMGTRV 179
            Q R + ++PQ+I  IQ II +G+AY  +  + FD    P +YG    ++ + Q+ G  V
Sbjct: 149 VQTRVSEYVPQIIKFIQKIIDNGYAYAVDGSVYFDVDKFPHSYGKLVGQRKNLQE-GEGV 207

Query: 180 PEKYHKKNPADFILWKRSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLD 239
                K++PADF LWK S P EP WESPWG+GRPGWHIECSAM+S  LG   DIHGGG+D
Sbjct: 208 LSDSRKRSPADFALWKASKPGEPSWESPWGKGRPGWHIECSAMASAILGSQLDIHGGGID 267

Query: 240 LIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGG 299
           L FPHHENEIAQS  A    +  N ++H G L + G KMSKS  NFITI E L  KK+  
Sbjct: 268 LAFPHHENEIAQSEAAFDDSQWVNYFLHTGHLTINGEKMSKSLKNFITIKEAL--KKYSP 325

Query: 300 RSWPAPVIRLAMLMTHYREPIDFTVQRLTEAEILLS----------------KWPQTSTS 343
           R      +RLA L+  +R P+D++   + +A  L                  K  +  + 
Sbjct: 326 R-----QLRLAFLLHQWRSPLDYSDSTMEQALQLEKSLNNFFLDVKALLRGAKPFEKLSE 380

Query: 344 K--------GIIDPAVLSALYNDLNTVSAIQALHKL---------ARESTKNHDLLPIFN 386
           K        G    AV +AL ++ +T   ++A+ +L               N  LL    
Sbjct: 381 KEAELLEDFGKTQTAVHAALCDNFDTPRVMEAIRELVSQGNAYIRESGERPNSALLKAIA 440

Query: 387 AS----AHILGIEVCKE---------HLNKNISIAIEKLVQERLILLKMKKFSSA-DYIR 432
           +       I G+   K                     + V+E     K+ +     D +R
Sbjct: 441 SYITKLLKIFGLSEGKGQQYVLEATVMPYVQSLSEFREKVREVAREKKVPEILELCDTLR 500

Query: 433 -KQLESKGFILEDYKNP 448
              L   G  LED K  
Sbjct: 501 DSDLLELGVRLEDRKGS 517


>gnl|CDD|110410 pfam01406, tRNA-synt_1e, tRNA synthetases class I (C) catalytic
           domain.  This family includes only cysteinyl tRNA
           synthetases.
          Length = 301

 Score =  372 bits (957), Expect = e-103
 Identities = 145/315 (46%), Positives = 197/315 (62%), Gaps = 17/315 (5%)

Query: 17  EFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGEKCVTYVRNITDID 76
            F  +    + MYVCGPTVYD +HIG+AR  + FDVL R L+    +  V +V+N TDID
Sbjct: 1   FFVPLHQGKVNMYVCGPTVYDDSHIGHARSAVAFDVLRRYLQALGYD--VQFVQNFTDID 58

Query: 77  DKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQPRATNHIPQMIYLI 136
           DKII+RA+Q+  S         + ++    + KD   L  L P  +PR T HI ++I  I
Sbjct: 59  DKIIKRAQQQGESFRE------LAARFITAYTKDMDALNVLPPDLEPRVTEHIDEIIEFI 112

Query: 137 QNIILHGHAYEA-NNEIIFDTSSIPNYGSFSRRKIDEQKMGTRVPEKYHKKNPADFILWK 195
           + +I  G+AY + N ++ FD SS P+YG  S + +++ + G R      K++P DF LWK
Sbjct: 113 ERLIKKGYAYVSDNGDVYFDVSSFPDYGKLSGQNLEQLEAGARGEVGEGKRDPLDFALWK 172

Query: 196 RSTPMEPGWESPWGRGRPGWHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCA 255
            S   EP W+SPWG+GRPGWHIECSAM+  YLG   DIHGGG+DL FPHHENEIAQS  A
Sbjct: 173 ASKEGEPSWDSPWGKGRPGWHIECSAMARKYLGSQIDIHGGGVDLKFPHHENEIAQSEAA 232

Query: 256 DRIEKTANIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTH 315
              +  A  W+HNG L +EG KMSKS GNF+TI ++L  K++  R     ++R  +L  H
Sbjct: 233 FDQQ-LAKYWLHNGHLMIEGEKMSKSLGNFLTIRDVL--KRYDPR-----ILRYFLLSVH 284

Query: 316 YREPIDFTVQRLTEA 330
           YR P+DF+ + L +A
Sbjct: 285 YRSPLDFSEELLEQA 299


>gnl|CDD|173899 cd00672, CysRS_core, catalytic core domain of cysteinyl tRNA
           synthetase.  Cysteinyl tRNA synthetase (CysRS) catalytic
           core domain. This class I enzyme is a monomer which
           aminoacylates the 2'-OH of the nucleotide at the 3' of
           the appropriate tRNA. The core domain is based on the
           Rossman fold and is responsible for the ATP-dependent
           formation of the enzyme bound aminoacyl-adenylate. It
           contains the characteristic class I HIGH and KMSKS
           motifs, which are involved in ATP binding.
          Length = 213

 Score =  174 bits (443), Expect = 5e-44
 Identities = 63/109 (57%), Positives = 78/109 (71%), Gaps = 8/109 (7%)

Query: 215 WHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE 274
           WHIECSAM+  YLG+ FDIHGGG+DLIFPHHENEIAQS  A   +  A  W+H G L ++
Sbjct: 113 WHIECSAMAMKYLGETFDIHGGGVDLIFPHHENEIAQSEAA-TGKPFARYWLHTGHLTID 171

Query: 275 GRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDFT 323
           G KMSKS GNFIT+ + L  KK+        V+RLA+L +HYR P+DF+
Sbjct: 172 GEKMSKSLGNFITVRDAL--KKYDPE-----VLRLALLSSHYRSPLDFS 213



 Score =  151 bits (385), Expect = 3e-37
 Identities = 59/125 (47%), Positives = 77/125 (61%), Gaps = 11/125 (8%)

Query: 6   KIYNTLERKITEFQAIDPSNIRMYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYY-YGEK 64
           ++YNTL R+  EF  ++P  + MYVCGPTVYD+AHIG+AR  +VFDVL R L    Y   
Sbjct: 1   RLYNTLTRQKEEFVPLNPGLVTMYVCGPTVYDYAHIGHARTYVVFDVLRRYLEDLGYK-- 58

Query: 65  CVTYVRNITDIDDKIIERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAPTHQPR 124
            V YV+NITDIDDKII+RAR+E   +   +    +    T++F +D   L  L P   PR
Sbjct: 59  -VRYVQNITDIDDKIIKRAREEG--LSWKE----VADYYTKEFFEDMKALNVLPPDVVPR 111

Query: 125 ATNHI 129
              HI
Sbjct: 112 VW-HI 115


>gnl|CDD|153417 cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl
           tRNA synthetases.  This domain is found in cysteinyl
           tRNA synthetases (CysRS), which belong to the class Ia
           aminoacyl tRNA synthetases. It lies C-terminal to the
           catalytic core domain, and recognizes and specifically
           binds to the tRNA anticodon. CysRS catalyzes the
           transfer of cysteine to the 3'-end of its tRNA.
          Length = 156

 Score = 56.8 bits (138), Expect = 1e-08
 Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 16/108 (14%)

Query: 353 SALYNDLNTVSAIQALHKLARE----STKNHDLLPIFNAS----AHILGI--EVCKEHLN 402
           +A+ +D NT  A+  L +LARE      ++ +      A       +LG+  +  +  L 
Sbjct: 40  AAMDDDFNTPEALAVLFELAREINRLKKEDIEKAAALAALLKALGGVLGLLQQDPEAFLQ 99

Query: 403 KNISI------AIEKLVQERLILLKMKKFSSADYIRKQLESKGFILED 444
                       IE L+ +R    K K ++ AD IR +L ++G ILED
Sbjct: 100 GGTGEGGLSVAEIEALIAQRNQARKAKDWAEADRIRDELAAQGIILED 147


>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
           acyl-tRNA synthetase.  Class I amino acyl-tRNA
           synthetase (aaRS) catalytic core domain. These enzymes
           are mostly monomers which aminoacylate the 2'-OH of the
           nucleotide at the 3' of the appropriate tRNA. The core
           domain is based on the Rossman fold and is responsible
           for the ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding.
          Length = 143

 Score = 51.7 bits (124), Expect = 4e-07
 Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 4/69 (5%)

Query: 214 GWHIECSAMSSHYLGKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNL 273
            +    +A          DIH GG D +  H E  +     A          +  G +  
Sbjct: 77  EYMFLQAADFLLLYETECDIHLGGSDQLG-HIELGLELLKKAGG--PARPFGLTFGRVMG 133

Query: 274 E-GRKMSKS 281
             G KMSKS
Sbjct: 134 ADGTKMSKS 142



 Score = 47.9 bits (114), Expect = 7e-06
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 28 MYVCGPTVYDFAHIGNARPMIVFDVLYRLLRYYYGEKCVTYVRNITDIDDKIIERA 83
              G T   + HIG+ R ++ FD L +  R    +  V  +  I D    I + A
Sbjct: 1  TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYK--VRCIALIDDAGGLIGDPA 54


>gnl|CDD|30409 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 933

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 35/132 (26%), Positives = 63/132 (47%), Gaps = 17/132 (12%)

Query: 266 IHNGF-LNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDFTV 324
           + +GF L+ +GRKMSKS GN +   +++   K+G     A ++RL +  + Y E + F+ 
Sbjct: 590 LTHGFVLDEKGRKMSKSLGNVVDPQDVI--DKYG-----ADILRLWVASSDYWEDLRFSD 642

Query: 325 QRLTEAEILLSKWPQT----STSKGIIDPAVLSALYNDLNT-----VSAIQALHKLARES 375
           + L +   +  K   T      +    DP   + L  +L       +S + +L K  RE+
Sbjct: 643 EILKQVREVYRKIRNTYRFLLGNLDDFDPKKDAVLPEELRELDRWILSRLNSLVKEVREA 702

Query: 376 TKNHDLLPIFNA 387
            +N+D   +  A
Sbjct: 703 YENYDFHKVVRA 714


>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
           synthetases.  Leucyl tRNA synthetase (LeuRS) catalytic
           core domain. This class I enzyme is a monomer which
           aminoacylates the 2'-OH of the nucleotide at the 3' of
           the appropriate tRNA. The core domain is based on the
           Rossman fold and is responsible for the ATP-dependent
           formation of the enzyme bound aminoacyl-adenylate. It
           contains the characteristic class I HIGH and KMSKS
           motifs, which are involved in ATP binding. In Aquifex
           aeolicus, the gene encoding LeuRS is split in two, just
           before the KMSKS motif. Consequently, LeuRS is a
           heterodimer, which likely superimposes with the LeuRS
           monomer found in most other organisms. LeuRS has an
           insertion in the core domain, which is subject to both
           deletions and rearrangements and thus differs between
           prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
           editing region hydrolyzes mischarged cognate tRNAs and
           thus prevents the incorporation of chemically similar
           amino acids.
          Length = 314

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 7/47 (14%)

Query: 266 IHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML 312
           I  G + LEG KMSKS GN +T +E +  KK+G     A   RL +L
Sbjct: 264 IVQGMVLLEGEKMSKSKGNVVTPDEAI--KKYG-----ADAARLYIL 303


>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
           synthetases.  Methionine tRNA synthetase (MetRS)
           catalytic core domain. This class I enzyme aminoacylates
           the 2'-OH of the nucleotide at the 3' of the appropriate
           tRNA. MetRS, which consists of the core domain and an
           anti-codon binding domain, functions as a monomer.
           However, in some species the anti-codon binding domain
           is followed by an EMAP domain. In this case, MetRS
           functions as a homodimer. The core domain is based on
           the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding.  As a result of a deletion event, MetRS has a
           significantly shorter core domain insertion than IleRS,
           ValRS, and LeuR.  Consequently, the MetRS insertion
           lacks the editing function.
          Length = 319

 Score = 43.3 bits (103), Expect = 1e-04
 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 7/46 (15%)

Query: 268 NGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLM 313
           +G+L +EG+KMSKS GN +  ++LLE        + A  +R  +L 
Sbjct: 271 HGYLTVEGKKMSKSRGNVVDPDDLLER-------YGADALRYYLLR 309


>gnl|CDD|30492 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 558

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 17/27 (62%), Positives = 21/27 (77%)

Query: 268 NGFLNLEGRKMSKSNGNFITINELLET 294
           +GFL LEG+KMSKS GN +  +ELLE 
Sbjct: 324 HGFLTLEGQKMSKSRGNVVDPDELLEQ 350



 Score = 28.7 bits (64), Expect = 3.7
 Identities = 8/26 (30%), Positives = 11/26 (42%)

Query: 33 PTVYDFAHIGNARPMIVFDVLYRLLR 58
          P      H+G+    +  DV  R LR
Sbjct: 14 PYPNGPPHLGHLYTYLAADVYARYLR 39


>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
           isoleucyl, leucyl, valyl and methioninyl tRNA
           synthetases.  Catalytic core domain of isoleucyl,
           leucyl, valyl and methioninyl tRNA synthetases. These
           class I enzymes are all monomers. However, in some
           species, MetRS functions as a homodimer, as a result of
           an additional C-terminal domain. These enzymes
           aminoacylate the 2'-OH of the nucleotide at the 3' of
           the appropriate tRNA. The core domain is based on the
           Rossman fold and is responsible for the ATP-dependent
           formation of the enzyme bound aminoacyl-adenylate. It
           contains the characteristic class I HIGH and KMSKS
           motifs, which are involved in ATP binding.  Enzymes in
           this subfamily share an insertion in the core domain,
           which is subject to both deletions and rearrangements.
           This editing region hydrolyzes mischarged cognate tRNAs
           and thus prevents the incorporation of chemically
           similar amino acids. MetRS has a significantly shorter
           insertion, which lacks the editing function.
          Length = 312

 Score = 41.3 bits (97), Expect = 6e-04
 Identities = 55/303 (18%), Positives = 92/303 (30%), Gaps = 56/303 (18%)

Query: 33  PTVYDFAHIGNARPMIVFDVL--YRLLRYYY----------GEKCVTYVRNITDIDDKII 80
           P      H+G+A   I+ D +  Y+ +R Y           G               K I
Sbjct: 9   PYANGSLHLGHALTHIIADFIARYKRMRGYEVPFLPGWDTHGLPIELKAERKGGRKKKTI 68

Query: 81  ERARQEHPSIPINDAISIITSKNTQQFVKDTTRLACLAP------THQPRATNHIPQMIY 134
                        +       + + +  +D  RL           T +P    +   +  
Sbjct: 69  WIEE-------FREDPKEFVEEMSGEHKEDFRRLGISYDWSDEYITTEPE---YSKAVEL 118

Query: 135 LIQNIILHGHAYEANNEIIFDTSSIPNYGSFSRRKIDEQKMGTRVPEKYHKKNPA---DF 191
           +   +   G  Y   + +        +   F  + +   + G  VPE    +  A     
Sbjct: 119 IFSRLYEKGLIYRGTHPVRITEQWFFDMPKFKEKLLKALRRGKIVPEHVKNRMEAWLESL 178

Query: 192 ILWKRSTPMEPGWESPWGRGRPGWHIEC-------SAMSSHYL--GKVF------DIHGG 236
           + W  S          WG   P    +           S  Y    + F      D H  
Sbjct: 179 LDWAISRQR------YWGTPLPEDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYPADWHLI 232

Query: 237 GLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE-GRKMSKSNGNFITINELLETK 295
           G D++       I             N+ +H GF+  E G+KMSKS GN I  ++++E  
Sbjct: 233 GKDILRGWANFWITMLVALFGEIPPKNLLVH-GFVLDEGGQKMSKSKGNVIDPSDVVE-- 289

Query: 296 KFG 298
           K+G
Sbjct: 290 KYG 292


>gnl|CDD|35658 KOG0437, KOG0437, KOG0437, Leucyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 1080

 Score = 37.3 bits (86), Expect = 0.008
 Identities = 17/31 (54%), Positives = 21/31 (67%), Gaps = 2/31 (6%)

Query: 268 NGFLNLEGRKMSKSNGNFITINELLETKKFG 298
           NG L L   KMSKS GNF+T+ + +E  KFG
Sbjct: 701 NGHLMLNSEKMSKSTGNFMTLEQAIE--KFG 729


>gnl|CDD|30871 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 877

 Score = 36.0 bits (83), Expect = 0.023
 Identities = 32/135 (23%), Positives = 60/135 (44%), Gaps = 13/135 (9%)

Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAM-LMTHYREPID 321
           +++IH    + +GRKMSKS GN I   ++++  K+G     A  +R  +  +      I+
Sbjct: 511 DVYIHGLVRDEQGRKMSKSKGNVIDPLDVID--KYG-----ADALRFTLASLASPGRDIN 563

Query: 322 FTVQRLTEAEILLSK-WPQTSTSKGIIDPAVLSALYNDLNTVSA---IQALHKLARESTK 377
           F  +R+      L+K W  T      +D      L     +++    +  L++  +E T+
Sbjct: 564 FDEKRVEGYRNFLNKLWNATRFVLMNLDDLGPDDLDLLALSLADRWILSRLNETVKEVTE 623

Query: 378 NHDLLPIFNASAHIL 392
             D    F+ +A  L
Sbjct: 624 ALDNYR-FDEAARAL 637


>gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 577

 Score = 35.6 bits (82), Expect = 0.032
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 18/92 (19%)

Query: 258 IEKTANIWIHNGF---LNLEGRKMSKSNGNFITINELLE----------TKKFGGRSWPA 304
                 + +H G       EG KMS   GN +T+++LL+           +K       A
Sbjct: 361 YGPDKEVLLHQGVGLVRGGEGVKMSTRAGNVVTLDDLLDEAGERAPEEMEEKEEKNEEIA 420

Query: 305 PV-----IRLAMLMTHYREPIDFTVQRLTEAE 331
            V     +R A L     +   F   +    E
Sbjct: 421 EVVGIDAVRYADLSRSRDKDYVFDWDKALSFE 452



 Score = 27.1 bits (60), Expect = 9.4
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 40  HIGNARPMIVFDVLYRLLRYY 60
           HIG+ R  I+ D L R+L + 
Sbjct: 133 HIGHLRNAIIGDSLARILEFL 153


>gnl|CDD|145212 pfam01921, tRNA-synt_1f, tRNA synthetases class I (K).  This family
           includes only lysyl tRNA synthetases from prokaryotes.
          Length = 355

 Score = 34.5 bits (80), Expect = 0.064
 Identities = 14/24 (58%), Positives = 14/24 (58%)

Query: 270 FLNLEGRKMSKSNGNFITINELLE 293
            L   G KMS S GN ITI E LE
Sbjct: 271 ILLKGGGKMSSSKGNGITIEEWLE 294


>gnl|CDD|30841 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 814

 Score = 34.5 bits (79), Expect = 0.065
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 8/48 (16%)

Query: 266 IHNGF-LNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML 312
           I  G  L  EG KMSKS GN +   E +E  K+G     A  +RL ++
Sbjct: 567 ITQGMVLGEEGEKMSKSKGNVVDPEEAVE--KYG-----ADTVRLYIM 607


>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA
           synthetases.  Valine amino-acyl tRNA synthetase (ValRS)
           catalytic core domain. This enzyme is a monomer which
           aminoacylates the 2'-OH of the nucleotide at the 3' of
           the appropriate tRNA. The core domain is based on the
           Rossman fold and is responsible for the ATP-dependent
           formation of the enzyme bound aminoacyl-adenylate. It
           contains the characteristic class I HIGH and KMSKS
           motifs, which are involved in ATP binding.  ValRS has an
           insertion in the core domain, which is subject to both
           deletions and rearrangements. This editing region
           hydrolyzes mischarged cognate tRNAs and thus prevents
           the incorporation of chemically similar amino acids.
          Length = 382

 Score = 33.8 bits (78), Expect = 0.12
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 7/51 (13%)

Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLM 313
            +++H    + +GRKMSKS GN I   ++++   +G     A  +R  +  
Sbjct: 329 EVYLHGLVRDEDGRKMSKSLGNVIDPLDVID--GYG-----ADALRFTLAS 372


>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of  class I
           lysyl tRNA synthetase.  Class I lysyl tRNA synthetase
           (LysRS) catalytic core domain. This class I enzyme is a
           monomer which aminoacylates the 2'-OH of the nucleotide
           at the 3' of the appropriate tRNA. The core domain is
           based on the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding. The class I LysRS is found only in archaea and
           some bacteria and has evolved separately from class II
           LysRS, as the two do not share structural or sequence
           similarity.
          Length = 353

 Score = 33.1 bits (76), Expect = 0.18
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 11/64 (17%)

Query: 270 FLNLEGR-KMSKSNGNFITINELLETKKFGGRSWPAPVIRLAML---MTHYREPIDFTVQ 325
           F+ L+G  KMS S GN IT ++ LE         P  V+R               D  + 
Sbjct: 267 FIGLKGGGKMSSSKGNVITPSDWLEV-------APPEVLRYLYARRKNPEKHIGFDLDIL 319

Query: 326 RLTE 329
           RL +
Sbjct: 320 RLYD 323


>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
           synthetases.  Isoleucine amino-acyl tRNA synthetases
           (IleRS) catalytic core domain . This class I enzyme is a
           monomer which aminoacylates the 2'-OH of the nucleotide
           at the 3' of the appropriate tRNA. The core domain is
           based on the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding.  IleRS has an insertion in the core domain,
           which is subject to both deletions and rearrangements.
           This editing region hydrolyzes mischarged cognate tRNAs
           and thus prevents the incorporation of chemically
           similar amino acids.
          Length = 338

 Score = 32.6 bits (75), Expect = 0.25
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 8/50 (16%)

Query: 266 IHNGFLNLE-GRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMT 314
           I +GF+  E GRKMSKS GN++   E+++  K+G     A  +RL +  +
Sbjct: 287 IVHGFVLDEDGRKMSKSLGNYVDPQEVVD--KYG-----ADALRLWVASS 329


>gnl|CDD|143905 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
           Other tRNA synthetase sub-families are too dissimilar to
           be included.
          Length = 606

 Score = 32.3 bits (74), Expect = 0.27
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 7/54 (12%)

Query: 263 NIWIHNGFLNLEGRKMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHY 316
           N+ +H    + +GRKMSKS GN   I+ L    K+G     A  +RL +  + Y
Sbjct: 553 NVLVHGLVRDEQGRKMSKSLGN--VIDPLDVIDKYG-----ADALRLWLASSDY 599


>gnl|CDD|31574 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
           ribosomal structure and biogenesis].
          Length = 521

 Score = 30.2 bits (68), Expect = 1.3
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 8/54 (14%)

Query: 270 FLNLEGR-KMSKSNGNFITINELLETKKFGGRSWPAPVIRLAMLMTHYREPIDF 322
           ++ L+G  KMS S GN I++++ LE         P  V+R  +  T     IDF
Sbjct: 269 WILLKGGGKMSSSKGNVISLSDWLEV-------APPEVLRYLIARTKPNRHIDF 315


>gnl|CDD|36247 KOG1029, KOG1029, KOG1029, Endocytic adaptor protein intersectin
           [Signal transduction mechanisms, Intracellular
           trafficking, secretion, and vesicular transport].
          Length = 1118

 Score = 30.1 bits (67), Expect = 1.5
 Identities = 12/29 (41%), Positives = 15/29 (51%)

Query: 187 NPADFILWKRSTPMEPGWESPWGRGRPGW 215
            P D I+   S   EPGW +   RG+ GW
Sbjct: 713 EPGDIIIVFESQAAEPGWLAGELRGKTGW 741


>gnl|CDD|114364 pfam05636, DUF795, Protein of unknown function (DUF795).  This
           family consists of several bacterial proteins of unknown
           function.
          Length = 389

 Score = 29.7 bits (67), Expect = 2.0
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 388 SAHILGIEVCK--EHLNKNIS-IAIEKLVQERLILLKMKKFSSADYIRKQLESKG 439
             +ILG+E  K  +    NI    I++       L    +F+SA  IRK L+ K 
Sbjct: 161 PNNILGLEYAKAIKKAGSNIKLYTIKREGAGYHDLELEDQFASATAIRKALKEKD 215


>gnl|CDD|35654 KOG0433, KOG0433, KOG0433, Isoleucyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 937

 Score = 29.2 bits (65), Expect = 2.3
 Identities = 30/164 (18%), Positives = 61/164 (37%), Gaps = 21/164 (12%)

Query: 264 IWIHNGFLNLEGRKMSKSNGNFIT----INELLETKKFGGRSWPAPVIRLAMLMTHYREP 319
           + +H   L+  G KMSKS GN +      +  L+   +G     A  +R  +  +     
Sbjct: 600 VIVHGFTLDENGNKMSKSLGNVVDPTMVTDGSLKQPAYG-----ADGLRFWVAGSENTGE 654

Query: 320 IDFTVQRLTEAEILLSKWPQTST-SKGII---DPAVLSALYNDLNTVS--AIQALHKLAR 373
                + L + +  L K+  T     G +   D   +     DL  +    +Q L  + +
Sbjct: 655 SKIGPKILDQVDEKLIKFRNTFRFLLGNLQDFDGKQVKFPLKDLRYIDQYMLQQLDAIVK 714

Query: 374 ESTKNHDLLPIFNASAHILGIEVCKEHLNKNISIAIEKLVQERL 417
              + ++          +      ++ L +N+S     +V++RL
Sbjct: 715 RIIELYNDYKFRKVVNDL------QQFLQRNLSAFYFDIVKDRL 752


>gnl|CDD|111812 pfam02964, MeMO_Hyd_G, Methane monooxygenase, hydrolase gamma
           chain. 
          Length = 160

 Score = 28.7 bits (64), Expect = 3.1
 Identities = 12/25 (48%), Positives = 19/25 (76%)

Query: 409 IEKLVQERLILLKMKKFSSADYIRK 433
           IE+ ++E+L +LK +KF+ AD I K
Sbjct: 51  IERKIEEKLAVLKTEKFNVADLITK 75


>gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal
           transduction mechanisms].
          Length = 382

 Score = 28.8 bits (64), Expect = 3.3
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 7/53 (13%)

Query: 342 TSKGIIDPAVLSALYNDLNTVSAIQALHKLARESTKNHDLLPIFNASAHILGI 394
           T KGI+   V++   +      A++ + +LA E       LP+ +A+  ++GI
Sbjct: 316 TVKGIMTTPVVTVRPDT----PAVELVPRLADEG---LHALPVLDAAGKLVGI 361


>gnl|CDD|35653 KOG0432, KOG0432, KOG0432, Valyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 995

 Score = 28.7 bits (64), Expect = 3.8
 Identities = 10/13 (76%), Positives = 10/13 (76%)

Query: 274 EGRKMSKSNGNFI 286
            GRKMSKS GN I
Sbjct: 590 HGRKMSKSLGNVI 602


>gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases
           (Fe-ADH)-like.  Large metal-containing  alcohol
           dehydrogenases (ADH), known as iron-containing alcohol
           dehydrogenases. They contain a dehydroquinate
           synthase-like protein structural fold and mostly contain
           iron. They are distinct from other alcohol
           dehydrogenases which contains different protein domains.
           There are several distinct families of alcohol
           dehydrogenases: Zinc-containing long-chain alcohol
           dehydrogenases; insect-type, or short-chain alcohol
           dehydrogenases; iron-containing alcohol dehydrogenases,
           and others. The iron-containing family has a Rossmann
           fold-like topology that resembles the fold of the
           zinc-dependent alcohol dehydrogenases, but lacks
           sequence homology, and differs in strand arrangement.
           ADH catalyzes the reversible oxidation of alcohol to
           acetaldehyde with the simultaneous reduction of NAD(P)+
           to NAD(P)H.
          Length = 370

 Score = 28.0 bits (63), Expect = 5.1
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 219 CSAMSSHYLGKVFDI-HGGGLDLIFPHHENEIAQSCCADRIEKTANIWIHNGFLNLE 274
             AM+ H LG ++ I HG    ++ PH     A++   ++    A         + +
Sbjct: 254 VHAMA-HPLGALYHIPHGLANAILLPHVMRFNAEA-IPEKYADIARAMGKVSGGSDD 308


>gnl|CDD|173969 cd08148, RuBisCO_large, Ribulose bisphosphate carboxylase large
           chain.  Ribulose bisphosphate carboxylase (Rubisco)
           plays an important role in the Calvin reductive pentose
           phosphate pathway. It catalyzes the primary CO2 fixation
           step. Rubisco is activated by carbamylation of an active
           site lysine, stabilized by a divalent cation, which then
           catalyzes the proton abstraction from the substrate
           ribulose 1,5 bisphosphate (RuBP) and leads to the
           formation of two molecules of 3-phosphoglycerate.
           Members of the Rubisco family can be divided into 4
           subgroups, Form I-IV, which differ in their taxonomic
           distribution and subunit composition. Form I-III have
           Rubisco activity, while Form IV, also called
           Rubisco-like proteins (RLP), are missing critical active
           site residues and therefore do not catalyze CO2
           fixation. They are believed to utilize a related
           enzymatic mechanism, but have divergent functions.
          Length = 366

 Score = 27.8 bits (62), Expect = 7.0
 Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)

Query: 49  VFDVLYRLLRYYYGEKCVTYVRNITDIDDKIIERA 83
           V   L R+ +   GEK +  V N+T    +IIERA
Sbjct: 181 VAAALDRV-QEETGEKKLYAV-NVTAGTFEIIERA 213


>gnl|CDD|32162 COG1979, COG1979, Uncharacterized oxidoreductases, Fe-dependent
           alcohol dehydrogenase family [Energy production and
           conversion].
          Length = 384

 Score = 27.5 bits (61), Expect = 7.8
 Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 5/38 (13%)

Query: 209 GRGRPG-WHIECSAMSSHYLGKVFDI-HGGGLDLIFPH 244
           G G P  W    + M  H L  ++DI H  GL ++ P 
Sbjct: 254 GAGVPQDW---ATHMIGHELTALYDIDHAQGLAIVLPA 288


>gnl|CDD|37109 KOG1898, KOG1898, KOG1898, Splicing factor 3b, subunit 3 [RNA
           processing and modification].
          Length = 1205

 Score = 27.2 bits (60), Expect = 8.6
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 228 GKVFDIHGGGLDLIFPHHENEIAQSCCADRIEKTANIWIH 267
            +VFD   G +  +    +NE A S CA     +      
Sbjct: 855 IRVFDPKSGKIICLVELGQNEAAFSVCAVDFSSSEYQPFV 894


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.320    0.136    0.415 

Gapped
Lambda     K      H
   0.267   0.0692    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,833,313
Number of extensions: 314422
Number of successful extensions: 796
Number of sequences better than 10.0: 1
Number of HSP's gapped: 775
Number of HSP's successfully gapped: 44
Length of query: 461
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 364
Effective length of database: 4,167,664
Effective search space: 1517029696
Effective search space used: 1517029696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)