Alignments for a candidate for dapF in Shewanella sp. ANA-3

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate 7023157 Shewana3_0391 diaminopimelate epimerase (RefSeq)

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__ANA3:7023157
          Length = 275

 Score =  394 bits (1012), Expect = e-114
 Identities = 189/274 (68%), Positives = 217/274 (79%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           +QF+KMHGLGNDFMVVD VTQNVFFSPE IRRLADR+ G+GFDQLL+VEPPYDP+LDFHY
Sbjct: 2   IQFTKMHGLGNDFMVVDGVTQNVFFSPEQIRRLADRNFGIGFDQLLLVEPPYDPDLDFHY 61

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFNADG EV  CGNGARCFARFVR KGLTNK  IRVST+ G+M L +  D  V VNMG 
Sbjct: 62  RIFNADGGEVENCGNGARCFARFVRNKGLTNKNKIRVSTSAGKMTLRLERDGTVTVNMGV 121

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P  +PS +PF+A KAEKTY+++  +QT LCG  SMGNPHCV+ V+DV  A V  +G +L 
Sbjct: 122 PVLDPSQIPFKAKKAEKTYLLQTPQQTFLCGAASMGNPHCVLDVEDVANANVAEIGALLT 181

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
            HERFP   N+GFMQVV   HI+LRVYERGA ET ACG+GACAAV VG  QG L ++VRV
Sbjct: 182 KHERFPRGVNVGFMQVVNSGHIKLRVYERGAAETLACGTGACAAVVVGQIQGKLDQQVRV 241

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
           +LPGG L I W+G G PL+MTGPA HVYDG I L
Sbjct: 242 DLPGGTLTINWEGEGKPLWMTGPAQHVYDGQIQL 275


Lambda     K      H
   0.323    0.140    0.425 

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: 282
Number of extensions: 6
Number of successful extensions: 2
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: 275
Length adjustment: 25
Effective length of query: 249
Effective length of database: 250
Effective search space:    62250
Effective search space used:    62250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate 7023157 Shewana3_0391 (diaminopimelate epimerase (RefSeq))
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.17825.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.17825.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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