GapMind for Amino acid biosynthesis

 

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

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_04530 AO356_04530 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_04530
          Length = 292

 Score =  471 bits (1213), Expect = e-138
 Identities = 236/291 (81%), Positives = 258/291 (88%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MIAGSMVALVTP DAQG LDW SL+KLVDFHL+ GT+AIVAVGTTGESATLDV EHI+VI
Sbjct: 1   MIAGSMVALVTPMDAQGHLDWASLSKLVDFHLENGTHAIVAVGTTGESATLDVNEHIEVI 60

Query: 61  RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120
           R VV QV GRIPVIAGTGANSTREAV LT  AK  GADACLLV PYYNKPTQEG+YQHF+
Sbjct: 61  RAVVKQVNGRIPVIAGTGANSTREAVELTRNAKEAGADACLLVVPYYNKPTQEGLYQHFK 120

Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180
           HIAEAV IPQILYNVPGRTSCDM  ETV RLS VPNIIGIKEATGD++RAK +++ V KD
Sbjct: 121 HIAEAVDIPQILYNVPGRTSCDMQAETVIRLSTVPNIIGIKEATGDMKRAKAILDGVSKD 180

Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240
           F+V SGDD TAVEL+LLGGKGNISVTANVAPR M+DLC AA++GDA  ARAIN++LMPLH
Sbjct: 181 FIVLSGDDPTAVELILLGGKGNISVTANVAPREMADLCEAALKGDAETARAINEKLMPLH 240

Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
           K LFIE+NPIPVKWAL EMGL+ EGIRLPLTWLS  CHEPLRQA+RQ+GVL
Sbjct: 241 KDLFIEANPIPVKWALVEMGLMHEGIRLPLTWLSTPCHEPLRQALRQSGVL 291


Lambda     K      H
   0.319    0.134    0.393 

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: 347
Number of extensions: 9
Number of successful extensions: 1
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: 292
Length of database: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate AO356_04530 AO356_04530 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.1354.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1354.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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