GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Phaeobacter inhibens BS107

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate GFF3342 PGA1_c33950 diaminopimelate epimerase DapF

Query= curated2:Q3IZB6
         (279 letters)



>FitnessBrowser__Phaeo:GFF3342
          Length = 281

 Score =  298 bits (763), Expect = 9e-86
 Identities = 143/275 (52%), Positives = 193/275 (70%), Gaps = 2/275 (0%)

Query: 2   MDMGASSGLGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQ 61
           M +G+ + L FMKMHG GNDFVV+D+R +    +T  +A  +  R  G+GFDQL  I   
Sbjct: 4   MTIGSDTRLPFMKMHGLGNDFVVVDARDQTWD-ITPAMAEGIAHRQMGIGFDQLTVITKG 62

Query: 62  EGADCALDFWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVA 121
           +  D  L F+N+DGS S  CGNATRC++ +L+ + G+  + L T RG L A    +GL +
Sbjct: 63  D-EDAHLTFYNADGSTSAACGNATRCIARHLLDESGKTHLRLTTDRGLLLAEDAGNGLTS 121

Query: 122 VNMGAPQLLWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVE 181
           VNMG PQL W +IPLA  ++T  LP+EG P+A GMGNPHC +FV++AE + LA  GA  E
Sbjct: 122 VNMGEPQLDWQDIPLAEDVDTLELPIEGAPTATGMGNPHCTFFVDNAEVIPLAEFGARYE 181

Query: 182 TDPLFPERTNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRL 241
             PL+PERTNV+ A ++ PD LR+RVWERG GITLA GS +CATAVAAARRGLT R+V++
Sbjct: 182 HHPLYPERTNVQVAHVVAPDHLRMRVWERGVGITLASGSSSCATAVAAARRGLTSRKVQI 241

Query: 242 EMDGGVLEVDWRDEGVWLSGPVARVFEGHLSPEMM 276
           ++DGG L +DWR +GVW++GP   V +GH + + +
Sbjct: 242 DLDGGTLWIDWRKDGVWMTGPTMHVADGHFTRQFL 276


Lambda     K      H
   0.321    0.138    0.423 

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: 310
Number of extensions: 11
Number of successful extensions: 3
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: 279
Length of database: 281
Length adjustment: 26
Effective length of query: 253
Effective length of database: 255
Effective search space:    64515
Effective search space used:    64515
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: 47 (22.7 bits)

Align candidate GFF3342 PGA1_c33950 (diaminopimelate epimerase DapF)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.31059.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31059.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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