GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas simiae WCS417

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate GFF1410 PS417_07165 dihydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__WCS417:GFF1410
          Length = 292

 Score =  472 bits (1215), Expect = e-138
 Identities = 239/291 (82%), Positives = 260/291 (89%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MIAGSMVALVTP DAQG LDWDSL KLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI
Sbjct: 1   MIAGSMVALVTPMDAQGHLDWDSLGKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60

Query: 61  RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120
             VV +V GRI VIAGTGANSTREA+ LT+ AK  GADACLLVTPYYNKPTQEG+YQHFR
Sbjct: 61  EFVVKRVAGRIAVIAGTGANSTREAIELTKNAKKAGADACLLVTPYYNKPTQEGLYQHFR 120

Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180
            IAEAV IPQILYNVPGRT+CDM   TV RLS VPNIIGIKEATGDLQRAK+++  V  D
Sbjct: 121 AIAEAVDIPQILYNVPGRTACDMQAATVIRLSTVPNIIGIKEATGDLQRAKDILAGVSSD 180

Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240
           FLVYSGDDATAVEL+LLGGKGNISVTANVAPRAMS++CAAA+ GDA  ARAI+++LMPL+
Sbjct: 181 FLVYSGDDATAVELILLGGKGNISVTANVAPRAMSEMCAAAIAGDAVTARAIHEKLMPLN 240

Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
           K LFIESNPIPVKWAL EMG++P+GIRLPLT LS  CHEPLRQA+RQ+GVL
Sbjct: 241 KTLFIESNPIPVKWALTEMGMMPDGIRLPLTRLSEACHEPLRQALRQSGVL 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: 352
Number of extensions: 8
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 GFF1410 PS417_07165 (dihydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.29635.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29635.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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