GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Herbaspirillum seropedicae SmR1

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate HSERO_RS03030 HSERO_RS03030 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__HerbieS:HSERO_RS03030
          Length = 268

 Score =  291 bits (744), Expect = 1e-83
 Identities = 155/263 (58%), Positives = 190/263 (72%), Gaps = 1/263 (0%)

Query: 6   IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           + +A+AGA GRMGR LI+A L  + +QL  AL+   S  +G+DAG   G   TGV ++S 
Sbjct: 4   LNIAVAGASGRMGRMLIEAILNADDLQLAGALDTPTSPSIGTDAGLFLGKA-TGVLIESD 62

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           L       DV IDFTRPEGTL HL +C  HG  +VIGTTGF+  GK AI   A   AI+ 
Sbjct: 63  LARGLAKADVLIDFTRPEGTLKHLEYCAAHGVKVVIGTTGFEPEGKAAIAAYAEKTAIMA 122

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A N SVGVNV +KLLE AAK      DIEIIEAHHR KVDAPSGTAL MGE IA AL K 
Sbjct: 123 APNMSVGVNVTMKLLEMAAKNFSHGYDIEIIEAHHRFKVDAPSGTALKMGEVIADALGKK 182

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L D AVY+REG TGER P +IGFATVR GDI+G+HT +FA IGER+EI+HK+SSR+++A 
Sbjct: 183 LDDVAVYAREGVTGERDPSSIGFATVRGGDIIGDHTVLFAGIGERIEISHKSSSRVSYAM 242

Query: 246 GAVRSALWLSGKESGLFDMRDVL 268
           G++R+A +L+ KE+GL+DM+DVL
Sbjct: 243 GSLRAARYLADKETGLYDMQDVL 265


Lambda     K      H
   0.319    0.135    0.383 

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: 268
Number of extensions: 15
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: 273
Length of database: 268
Length adjustment: 25
Effective length of query: 248
Effective length of database: 243
Effective search space:    60264
Effective search space used:    60264
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 HSERO_RS03030 HSERO_RS03030 (dihydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.28088.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28088.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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