GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Acidovorax sp. GW101-3H11

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate Ac3H11_2576 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.25)

Query= SwissProt::Q9KRB0
         (426 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2576
          Length = 676

 Score =  436 bits (1120), Expect = e-126
 Identities = 240/435 (55%), Positives = 309/435 (71%), Gaps = 22/435 (5%)

Query: 4   LTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKLGVN 63
           L L P++  +GEV+LPGSKS+SNR LLLAAL++GTT + +LL SDD R ML+AL ++G  
Sbjct: 7   LDLPPLQAAAGEVHLPGSKSISNRVLLLAALSNGTTTVHDLLASDDTRVMLDALRQIGCT 66

Query: 64  YRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPRMKE 123
             +    +T  + GLG     + P +LFLGNAGTAMRPL AAL L  G++ L+G PRM E
Sbjct: 67  --VDEAGSTVRITGLGGRLPQS-PAKLFLGNAGTAMRPLTAALALLGGEFELSGVPRMHE 123

Query: 124 RPIGHLVDALRQAGAQIEYLEQENFPPLRI-QGTGLQ----AGTVTIDGSISSQFLTAFL 178
           RPIG L+DALRQ G QI+YL  E +PPL+I  G G+     A  + + G +SSQFLTA L
Sbjct: 124 RPIGDLIDALRQLGCQIDYLGNEGYPPLKIAHGQGVPSLALAEPIRVRGDVSSQFLTALL 183

Query: 179 MSAPLAQGK--VTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           M+ PLA G   + I++VGEL+SKPYI ITL ++ +FG+ V + ++Q F IPAG  Y SPG
Sbjct: 184 MALPLAAGTQAIVIEVVGELISKPYIAITLQLLARFGIVVGHQNWQRFTIPAGSRYQSPG 243

Query: 237 QFLVEGDASSASYFLAAAAIK-GGE----VKVTGIGKNSIQGDIQFADALEKMGAQIEWG 291
              VE DASSASYF+A  AI  GGE    +K+ G+G +SIQGDI+F +A   MGA +  G
Sbjct: 244 SIHVEADASSASYFIALGAIATGGEAQKSIKIQGVGLDSIQGDIRFVEAARAMGAVVTGG 303

Query: 292 DDYVIARRGE--LNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAM 349
            +++   RG   L A++LD NHIPDAAMT+A  AL+A+GTT + N+ +WRVKETDR+AAM
Sbjct: 304 PNWLQIERGAWPLKAIELDCNHIPDAAMTLAVMALYAEGTTTLTNIASWRVKETDRIAAM 363

Query: 350 ATELRKVGATVEEGEDFIVITPPTKLIH---AAIDTYDDHRMAMCFSLVALSDT--PVTI 404
           ATELRK+GATVEEG D+I +TPPT+      A+I TYDDHR+AMCFSL A +    PV I
Sbjct: 364 ATELRKLGATVEEGADYIRVTPPTQAADWKAASIHTYDDHRVAMCFSLAAFNPARLPVRI 423

Query: 405 NDPKCTSKTFPDYFD 419
            DPKC +KTFPDYF+
Sbjct: 424 EDPKCVAKTFPDYFE 438


Lambda     K      H
   0.318    0.135    0.384 

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: 692
Number of extensions: 26
Number of successful extensions: 12
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: 426
Length of database: 676
Length adjustment: 35
Effective length of query: 391
Effective length of database: 641
Effective search space:   250631
Effective search space used:   250631
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_2576 (5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.25))
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.1068.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1068.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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