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_03200 AO356_03200 phospho-2-dehydro-3-deoxyheptonate aldolase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_03200
          Length = 358

 Score =  415 bits (1066), Expect = e-120
 Identities = 206/350 (58%), Positives = 259/350 (74%), Gaps = 1/350 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           +N++++   + L+TP+QLK   PLS      +   R+ I +I+ G D RL VV GPCSIH
Sbjct: 6   INDLNVASNETLITPDQLKRDIPLSDAALRTVTKGREVIRNILDGTDHRLFVVIGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           D + A EYA R K LAAEVSD+LYLVMRVYFEKPRTTVGWKGLINDP++D SF ++ GL 
Sbjct: 66  DIKAAHEYAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLH 125

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
           I R+LLL+L  MGLP ATEALDP SPQYL DL SWSAIGARTTESQTHREMASGLS  VG
Sbjct: 126 IGRQLLLDLAEMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVG 185

Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244
           FKNGTDG L  AINA+++ + PHRF+GINQ G V+++ T+GN  GHV+LRGG   PNY  
Sbjct: 186 FKNGTDGGLTVAINALQSVSSPHRFLGINQEGGVSIVTTKGNAYGHVVLRGGNGKPNYDS 245

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             VA CE+ + +A ++P++MVDCSH NSNKD   QP V E+V  QI +GN+SIIGLM+ES
Sbjct: 246 VSVALCEQALNKARIKPNIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVES 305

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           +++ G Q+  +  ++++YGVS+TDACI W  T+  LR +H  L   L  R
Sbjct: 306 HLNWGCQAIPKDLADLQYGVSITDACIDWSATENTLRSMHAKLKDVLPKR 355


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: 412
Number of extensions: 10
Number of successful extensions: 2
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: 358
Length adjustment: 29
Effective length of query: 327
Effective length of database: 329
Effective search space:   107583
Effective search space used:   107583
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_03200 AO356_03200 (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.19229.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19229.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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