GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Dechlorosoma suillum PS

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate Dsui_0649 Dsui_0649 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__PS:Dsui_0649
          Length = 276

 Score =  309 bits (791), Expect = 5e-89
 Identities = 154/274 (56%), Positives = 192/274 (70%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHGLGNDF+V+D V QN+  +P  +R LADR+ GVG DQ+L+VE P    +DF Y
Sbjct: 3   LEFTKMHGLGNDFVVLDGVRQNITLTPAQLRFLADRNFGVGCDQILLVEKPGQAGVDFRY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFNADGSEV QCGNGARCF RFV  +GLT+KR+I+V T +G +   +  D  V V+MG+
Sbjct: 63  RIFNADGSEVEQCGNGARCFVRFVHEQGLTDKREIKVETKSGIISPRLEADGNVTVDMGK 122

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P F P  +PF +        ++  +Q +    VSMGNPH V  V+DVDTA V   GP++E
Sbjct: 123 PVFAPDRIPFVSPTDAVIQPLQVGDQEVAITAVSMGNPHAVQVVEDVDTAPVAIQGPMIE 182

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
           SH RFP+R N GF+QVV R  +RLRVYERGAGET ACG+GACAAV  GI + LL   VRV
Sbjct: 183 SHPRFPQRVNAGFLQVVDRHSVRLRVYERGAGETLACGTGACAAVVAGISRDLLDSPVRV 242

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
              GG L IAW GPG P++MTGPAV V+ G I L
Sbjct: 243 STRGGELSIAWNGPGTPVHMTGPAVTVFSGEIEL 276


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: 271
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: 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 Dsui_0649 Dsui_0649 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.17091.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17091.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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