GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Pseudomonas fluorescens FW300-N2C3

Align 3-deoxy-7-phosphoheptulonate synthase, Tyr-sensitive (EC 2.5.1.54) (characterized)
to candidate AO356_00370 AO356_00370 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= ecocyc::AROF-MONOMER
         (356 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00370
          Length = 356

 Score =  358 bits (920), Expect = e-104
 Identities = 180/327 (55%), Positives = 228/327 (69%), Gaps = 4/327 (1%)

Query: 22  QLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHDPETALEYARRFKALA 81
           QLK   PLS     Q++  R++I  I+ G D RLLV+ GPCSIHDP++ALEYA     +A
Sbjct: 29  QLKHQLPLSTALSHQVSAHRQAIRAILNGEDARLLVIVGPCSIHDPKSALEYAANLARVA 88

Query: 82  AEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQIARKLLLELVNMGLPL 141
            EVSDS++LVMR Y EKPRTTVGWKGL  DP +DGS D+ AGL ++R+L+ E++ +GLP+
Sbjct: 89  HEVSDSMFLVMRAYVEKPRTTVGWKGLAYDPGLDGSDDMAAGLTLSRELMREMLQLGLPV 148

Query: 142 ATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGFKNGTDGSLATAINAM 201
           ATE L P +  Y  DL SW AIGARTTESQ HREMASGL MPVGFKNGTDG +  A +AM
Sbjct: 149 ATELLQPMAASYFDDLLSWVAIGARTTESQIHREMASGLGMPVGFKNGTDGGVGIACDAM 208

Query: 202 RAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPADVAQCEKEMEQAGLR 260
           R+AA PHR  G++  G  A++QT GNPD H++LRGG + PNY    V Q   ++ +  + 
Sbjct: 209 RSAAHPHRHFGVDSQGHPAIIQTPGNPDTHLVLRGGHRGPNYDRQSVTQIHSDLTRLKIP 268

Query: 261 PSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESNIHEGNQSSEQPRSEM 320
             +MVDCSH NS KD  RQP V + V+ Q   GNRS+IG+M+ES++ EG Q        M
Sbjct: 269 ARIMVDCSHANSGKDPLRQPQVFDDVLEQRLQGNRSLIGMMLESHLFEGCQPL---GPSM 325

Query: 321 KYGVSVTDACISWEMTDALLREIHQDL 347
           +YGVSVTD C+ WE T+ LLRE H+ L
Sbjct: 326 RYGVSVTDGCLGWESTEQLLREAHRRL 352


Lambda     K      H
   0.316    0.131    0.378 

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: 419
Number of extensions: 15
Number of successful extensions: 3
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: 356
Length of database: 356
Length adjustment: 29
Effective length of query: 327
Effective length of database: 327
Effective search space:   106929
Effective search space used:   106929
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: 49 (23.5 bits)

Align candidate AO356_00370 AO356_00370 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

Software error:

../bin/blast/fastacmd -i /tmp/list.29942.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29942.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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