GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Sphingomonas koreensis DSMZ 15582

Align glutamyl-tRNAGln amidotransferase subunit A (EC 6.3.5.7) (characterized)
to candidate Ga0059261_0082 Ga0059261_0082 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-)

Query= metacyc::MONOMER-13955
         (485 letters)



>FitnessBrowser__Korea:Ga0059261_0082
          Length = 494

 Score =  438 bits (1127), Expect = e-127
 Identities = 233/485 (48%), Positives = 324/485 (66%), Gaps = 10/485 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  ++  +   E    ++ D    ++ A   ++ AF+    + A A A+  D A      
Sbjct: 9   VAAIRDGVRSGEFTAIEVADAFITKVSAAK-QLNAFIVETPDHAIAAARTADAARAAGET 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L G+PIG+KD   TKG++TT +S +LE F P+Y++TV Q+L DA A  +GKLN+D+F
Sbjct: 68  LKPLAGVPIGMKDLFCTKGVQTTAASHMLEGFTPVYESTVSQKLWDAGAGMLGKLNLDQF 127

Query: 128 AMGSSTENSAYKLTKNPW------NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
           AMGSS E S +    +PW      N    PGGSSGGS++A+AA  VP + G+DTGGSIRQ
Sbjct: 128 AMGSSNETSYFGNVISPWRRKDGGNAALAPGGSSGGSSSAIAARLVPAATGTDTGGSIRQ 187

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+F G+ G+KPTYGR SR+G+VAFASSLDQ GP+ R V D A +L+A++G D  D+TS 
Sbjct: 188 PAAFTGISGIKPTYGRCSRWGVVAFASSLDQAGPMARDVRDCAIMLEAMAGFDPKDATSL 247

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
           ++ VP++ + L+ D++G K+ +PKEY  +G+  E        +  L+  GA   EVSLPH
Sbjct: 248 DMAVPNWEAGLSADLRGKKVGIPKEYRVDGMPAEIEALWQQGIDWLKDAGAEIVEVSLPH 307

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYR-TDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           +KYAL  YY+++ +EAS+NLAR+DG+RYG R   +  NL ++Y  TRA GFG EV+RRI+
Sbjct: 308 TKYALPAYYIIAPAEASSNLARYDGVRYGQRDLPDGANLQEMYAATRAAGFGPEVQRRIL 367

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           +GT+ LS+G+YDAYY +AQKVRTLI +DFE  + + D+++ PT P+ AF +GE + DPL 
Sbjct: 368 IGTYVLSAGFYDAYYTQAQKVRTLIAQDFEKAWAQCDLLLTPTAPSAAFALGEKSADPLA 427

Query: 421 MYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           MY ND+ T+P +LAG+P +SVP GL  DGLPLGLQIIGK FDE  V   + A EQ     
Sbjct: 428 MYLNDVFTVPSSLAGIPAMSVPGGLDKDGLPLGLQIIGKPFDEQGVLNASLAIEQRAG-F 486

Query: 480 KAKPE 484
            AKPE
Sbjct: 487 TAKPE 491


Lambda     K      H
   0.315    0.134    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 573
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 485
Length of database: 494
Length adjustment: 34
Effective length of query: 451
Effective length of database: 460
Effective search space:   207460
Effective search space used:   207460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Ga0059261_0082 Ga0059261_0082 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-))
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.19053.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19053.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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