GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Burkholderia phytofirmans PsJN

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate BPHYT_RS14895 BPHYT_RS14895 3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::Q9KRB0
         (426 letters)



>FitnessBrowser__BFirm:BPHYT_RS14895
          Length = 434

 Score =  503 bits (1294), Expect = e-147
 Identities = 265/436 (60%), Positives = 324/436 (74%), Gaps = 13/436 (2%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           ME L L P    SG + LPGSKS+SNR LLLAALA G T +TNLLDSDD R ML+AL KL
Sbjct: 1   MEFLDLGPFSRASGTIRLPGSKSISNRVLLLAALAEGETTITNLLDSDDTRVMLDALEKL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV  RL  D  TC V G   AF T +  +LFLGNAGTA+RPL AAL +  GDY + G PR
Sbjct: 61  GV--RLKRDGDTCVVTGTRGAF-TARTADLFLGNAGTAVRPLTAALAVNGGDYRIHGVPR 117

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGT-VTIDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GA+I+Y E E +PPLRI+   + A   +T+ G +SSQFLT+ LM
Sbjct: 118 MHERPIGDLVDGLRQLGARIDYEENEGYPPLRIRPGQINADAPITVRGDVSSQFLTSLLM 177

Query: 180 SAPLAQ---GKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           + PL +   G  T+++ GEL+SKPYI+IT+ +ME+FG++V  H + +FV+PAGQ Y SPG
Sbjct: 178 TLPLLRTESGVSTVQVDGELISKPYIEITIKLMERFGIKVERHGWHQFVVPAGQRYQSPG 237

Query: 237 QFLVEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVI 296
             +VEGDASSASYFLAA A+ GG ++V G+G+ SIQGD+ FADAL KMGA ++ GDD++ 
Sbjct: 238 TIMVEGDASSASYFLAAGALGGGPLRVEGVGRASIQGDVGFADALIKMGANLQMGDDWIE 297

Query: 297 AR-----RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMAT 351
            R      G+L  +D+D N IPDAAMTIA  ALFA G T +RN+ +WRVKETDRLAAMAT
Sbjct: 298 VRGVGHDSGKLEPIDMDCNLIPDAAMTIAVAALFADGATTLRNIASWRVKETDRLAAMAT 357

Query: 352 ELRKVGATVEEGEDFIVITPPTKLI-HAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCT 410
           ELRKVGA V+EGED++VI PP KL  +AAIDTYDDHRMAMCFSLV+L   PV INDPKC 
Sbjct: 358 ELRKVGAKVQEGEDYLVIEPPEKLTPNAAIDTYDDHRMAMCFSLVSLGGVPVRINDPKCV 417

Query: 411 SKTFPDYFDKFAQLSR 426
            KTFPDYF++F  L++
Sbjct: 418 GKTFPDYFERFTALAQ 433


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: 535
Number of extensions: 23
Number of successful extensions: 8
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: 434
Length adjustment: 32
Effective length of query: 394
Effective length of database: 402
Effective search space:   158388
Effective search space used:   158388
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: 51 (24.3 bits)

Align candidate BPHYT_RS14895 BPHYT_RS14895 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.21699.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21699.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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