GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Trichormus variabilis ATCC 29413

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_011317354.1 AVA_RS02395 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q3MFY8
         (278 letters)



>NCBI__GCF_000204075.1:WP_011317354.1
          Length = 278

 Score =  546 bits (1406), Expect = e-160
 Identities = 278/278 (100%), Positives = 278/278 (100%)

Query: 1   MTNQAPIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLE 60
           MTNQAPIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLE
Sbjct: 1   MTNQAPIPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLE 60

Query: 61  VPITNQLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQI 120
           VPITNQLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQI
Sbjct: 61  VPITNQLEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQI 120

Query: 121 QNLADFAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAI 180
           QNLADFAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAI
Sbjct: 121 QNLADFAEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAI 180

Query: 181 QTAELLAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQI 240
           QTAELLAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQI
Sbjct: 181 QTAELLAELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQI 240

Query: 241 YTLRHDTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278
           YTLRHDTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL
Sbjct: 241 YTLRHDTSDRACYMPGVLLAIRKVLQLKSLVYGLEKIL 278


Lambda     K      H
   0.317    0.136    0.386 

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: 446
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: 278
Length of database: 278
Length adjustment: 25
Effective length of query: 253
Effective length of database: 253
Effective search space:    64009
Effective search space used:    64009
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: 47 (22.7 bits)

Align candidate WP_011317354.1 AVA_RS02395 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.21828.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.21828.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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