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)