GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Magnetospirillum magneticum AMB-1

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_043745687.1 AMB_RS22745 4-hydroxy-tetrahydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>NCBI__GCF_000009985.1:WP_043745687.1
          Length = 265

 Score =  257 bits (656), Expect = 2e-73
 Identities = 131/265 (49%), Positives = 170/265 (64%)

Query: 6   IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           +R+ I G  GRMGR L++A L+ EG  L    ER GS ++G D G L G    G  V + 
Sbjct: 1   MRIGIVGCNGRMGRMLMEAVLSAEGCTLSGGTERAGSEVIGLDPGTLLGRPPVGALVTAD 60

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
              +    D  IDFT P  TL H A   + GK +V+GTTG  +  +  + +AA    +V+
Sbjct: 61  ARTLFQASDAVIDFTAPAATLAHAAIAAELGKVLVVGTTGLSKDDEARLAEAARSTPVVY 120

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A NFSVGVN+++ L E+AA ++GD  DIEI+E HHRHKVDAPSGTAL +G + A      
Sbjct: 121 APNFSVGVNLLMALTERAAAILGDDYDIEIVEMHHRHKVDAPSGTALGLGRSAALGRQVA 180

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L      +R+GHTG R  G IGFAT+R GD+VG+HT MFA  GER+E+THKASSR  FA 
Sbjct: 181 LDSRWCKARDGHTGARPKGEIGFATLRGGDVVGDHTVMFAAEGERVELTHKASSRTVFAK 240

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GAVR+A W +G++ GL+ MRDVL L
Sbjct: 241 GAVRAARWATGQKPGLYSMRDVLGL 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: 233
Number of extensions: 9
Number of successful extensions: 1
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: 265
Length adjustment: 25
Effective length of query: 248
Effective length of database: 240
Effective search space:    59520
Effective search space used:    59520
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 WP_043745687.1 AMB_RS22745 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.1687.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1687.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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