GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Sinorhizobium meliloti 1021

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate SMc01732 SMc01732 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__Smeli:SMc01732
          Length = 296

 Score =  326 bits (835), Expect = 4e-94
 Identities = 175/280 (62%), Positives = 208/280 (74%), Gaps = 10/280 (3%)

Query: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKI-DGQWVTHQWL 59
           +  L   IETAFE R  +       V R+AV   + LLDSG +RVAE+  DG W  +QWL
Sbjct: 17  LASLSQTIETAFEGRDAVNTGTRGAV-RDAVETALNLLDSGKVRVAERSEDGTWTVNQWL 75

Query: 60  KKAVLLSFRINDNQVIEGA--ESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFI 117
           KKAVLLSFR+N  +++ G   E+ ++DKV  KF  +    F+K GFR VP   VR+ A+I
Sbjct: 76  KKAVLLSFRLNPMELVRGGPGEAVWWDKVASKFDGWSVNEFEKAGFRAVPNCVVRRSAYI 135

Query: 118 ARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTI 177
           A N VLMPS+VN+GAYV EGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTI
Sbjct: 136 APNAVLMPSFVNLGAYVGEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTI 195

Query: 178 IEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGN 237
           IEDNCFIGARSEVVEG IV EGSV+ MGV+IG+ST+I DR TGE+ YG VP  SVVV+G+
Sbjct: 196 IEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVMYGEVPPYSVVVAGS 255

Query: 238 LPS----KDGK--YSLYCAVIVKKVDAKTRGKVGINELLR 271
           + S     +G+   +LYCAVIVK+VD KTR K GINELLR
Sbjct: 256 MASGSTMANGQPAPNLYCAVIVKRVDEKTRSKTGINELLR 295


Lambda     K      H
   0.318    0.136    0.391 

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: 288
Number of extensions: 11
Number of successful extensions: 4
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: 274
Length of database: 296
Length adjustment: 26
Effective length of query: 248
Effective length of database: 270
Effective search space:    66960
Effective search space used:    66960
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate SMc01732 SMc01732 (2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

Software error:

../bin/blast/fastacmd -i /tmp/list.21707.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21707.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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