GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Dechlorosoma suillum PS

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate Dsui_1942 Dsui_1942 cytidylate kinase/3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::Q9KRB0
         (426 letters)



>FitnessBrowser__PS:Dsui_1942
          Length = 644

 Score =  476 bits (1224), Expect = e-138
 Identities = 254/430 (59%), Positives = 310/430 (72%), Gaps = 7/430 (1%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           ME L L P     G V LPGSKS+SNR LLLAALA G T + +LL SDD   ML AL +L
Sbjct: 1   MEFLDLAPFVSAGGTVRLPGSKSISNRVLLLAALAEGVTEVRDLLHSDDTERMLEALQQL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV    S       + G+G  F   +  ELFLGNAGTA RPL AAL L  G YVL G  R
Sbjct: 61  GVGVE-SLGGEAYRITGVGGPFPVKEA-ELFLGNAGTAFRPLTAALALAGGHYVLKGVAR 118

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVT-IDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GA++ YL  + FPPL I    ++AG V  + G +SSQFLTA LM
Sbjct: 119 MHERPIGDLVDGLRQLGAEVRYLGNDGFPPLEIFPASIRAGGVLQVRGDVSSQFLTALLM 178

Query: 180 SAPLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFL 239
           + PL   +  +++VGEL+SKPYI+ITL  M +FGV+V    +Q FV+PAG  YVSPG   
Sbjct: 179 ALPLTGVETRVEVVGELISKPYIEITLATMARFGVEVQREGWQAFVVPAGVRYVSPGTVY 238

Query: 240 VEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIAR- 298
           VEGDASSASYFLAA AI GG ++V G+GK+SIQGD++FA+AL  MGA+IE G +++ AR 
Sbjct: 239 VEGDASSASYFLAAGAIGGGPLRVEGVGKDSIQGDVRFAEALALMGARIEMGPNWIEARA 298

Query: 299 --RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKV 356
              G+L A+DLD NHIPDAAMT+AT ALFA+GTT +RN+ +WRVKETDR+AAMATEL+K+
Sbjct: 299 PASGKLQAIDLDCNHIPDAAMTLATAALFAEGTTVLRNIASWRVKETDRIAAMATELQKL 358

Query: 357 GATVEEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPD 416
           GA VEEG D++ +TP   L  AAIDTYDDHRMAMCFSL A + TP+ INDPKC +KTFPD
Sbjct: 359 GAVVEEGPDYLKVTPVPALKPAAIDTYDDHRMAMCFSLAAFA-TPLRINDPKCVAKTFPD 417

Query: 417 YFDKFAQLSR 426
           YF++ A ++R
Sbjct: 418 YFERLATVTR 427


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: 669
Number of extensions: 31
Number of successful extensions: 7
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: 644
Length adjustment: 35
Effective length of query: 391
Effective length of database: 609
Effective search space:   238119
Effective search space used:   238119
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 Dsui_1942 Dsui_1942 (cytidylate kinase/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.8203.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8203.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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