Alignments for a candidate for dapF in Dyella japonica UNC79MFTsu3.2

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate N515DRAFT_3112 N515DRAFT_3112 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3112
          Length = 280

 Score =  275 bits (702), Expect = 1e-78
 Identities = 135/271 (49%), Positives = 181/271 (66%), Gaps = 1/271 (0%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++FSKMHG+GNDF++VDA         E IR LADRH GVGFDQL+ +EPP D    F+Y
Sbjct: 3   LRFSKMHGIGNDFVMVDARAAGFALDAEEIRALADRHAGVGFDQLISIEPPRDASCRFYY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKG-LTNKRDIRVSTANGRMVLTVTDDDLVRVNMG 119
            ++NADGS   QCGNG RC A ++   G LT    +R+ + +G + + +   D V V+MG
Sbjct: 63  GLWNADGSSANQCGNGVRCVAAWLHRAGELTLGETVRLESPSGPVTVRLLAADRVTVDMG 122

Query: 120 EPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVL 179
           EP F P+ +PF A    + Y +    QT+  G VSMGNPH V+ VDD+   A+  LGP L
Sbjct: 123 EPEFRPAQIPFDAAAPAERYALDTDGQTLEIGAVSMGNPHAVVTVDDLGAPALYRLGPAL 182

Query: 180 ESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVR 239
             H RF + AN GF+++V R H+RLRV+ERG+G T+ACG+GACAA+AV   +G + + V+
Sbjct: 183 TGHPRFAQGANAGFVRIVDRGHLRLRVHERGSGWTRACGTGACAAMAVLRLRGEVDDSVQ 242

Query: 240 VELPGGRLDIAWKGPGHPLYMTGPAVHVYDG 270
           V+LPGGRL I W GPGH L+MTGPA   ++G
Sbjct: 243 VDLPGGRLQIDWAGPGHTLWMTGPAAFAFEG 273


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: 285
Number of extensions: 14
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: 280
Length adjustment: 25
Effective length of query: 249
Effective length of database: 255
Effective search space:    63495
Effective search space used:    63495
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 N515DRAFT_3112 N515DRAFT_3112 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.28240.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.28240.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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