Alignments for a candidate for dapF in Methylosarcina fibrata AML-C10

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_020564745.1 A3OW_RS0117480 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>NCBI__GCF_000372865.1:WP_020564745.1
          Length = 276

 Score =  338 bits (867), Expect = 7e-98
 Identities = 163/271 (60%), Positives = 201/271 (74%)

Query: 3   FSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRI 62
           F+KMHGLGNDF+V+DA+TQ +  +PE IR+LADRHLG+GFDQLL+VE P     DF YRI
Sbjct: 4   FTKMHGLGNDFVVIDAMTQQIALTPERIRKLADRHLGIGFDQLLLVEKPVSGNADFKYRI 63

Query: 63  FNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPN 122
           FNADG EVAQCGNGARCFARFVR K L++K +IRV T +G+++L   +D+L+ VNMG P 
Sbjct: 64  FNADGGEVAQCGNGARCFARFVRDKRLSDKDEIRVDTDSGQLLLRFDEDNLITVNMGVPR 123

Query: 123 FEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESH 182
             P+ +P  A +    Y +    + +  G VSMGNPH VIQV DV  A V   G +LESH
Sbjct: 124 HTPAEIPLLAEREAAFYTVVIDGRELSFGAVSMGNPHAVIQVPDVSAAPVAETGRILESH 183

Query: 183 ERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVEL 242
             FPERANIGFMQ++ R HI+LRV+ERGA ET ACGSGACAA  +GI++  L  EVRVEL
Sbjct: 184 PLFPERANIGFMQIIDRNHIKLRVFERGAAETLACGSGACAAAVIGIERKQLDREVRVEL 243

Query: 243 PGGRLDIAWKGPGHPLYMTGPAVHVYDGFIH 273
           PGG L IAW G G P++MTGPA+ V++G IH
Sbjct: 244 PGGELKIAWAGRGKPVFMTGPAISVFEGIIH 274


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: 254
Number of extensions: 6
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: 274
Length of database: 276
Length adjustment: 25
Effective length of query: 249
Effective length of database: 251
Effective search space:    62499
Effective search space used:    62499
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 WP_020564745.1 A3OW_RS0117480 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.11366.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.11366.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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