GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Desulfovibrio vulgaris Miyazaki F

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate 8499684 DvMF_0450 dihydrodipicolinate reductase (RefSeq)

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__Miya:8499684
          Length = 259

 Score =  170 bits (431), Expect = 3e-47
 Identities = 105/264 (39%), Positives = 142/264 (53%), Gaps = 12/264 (4%)

Query: 8   VAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLD 67
           + + GAGGRMG  + + A     + L A +ER            LA          S  D
Sbjct: 5   IIVTGAGGRMGSTICRMAQEDPVLTLAAVVERPE---------RLASLDVWKCPSGSDPD 55

Query: 68  AVKDDFD--VFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           AV       V +DFT PE ++ +     + G   VIGTTG     K  + D A    I +
Sbjct: 56  AVFATVPGGVVVDFTSPEASMANARAAARAGVSHVIGTTGLTAEQKAELADLARTARIFW 115

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A N S+GVNV+LK+L +  + +G+  D+E++E HH  K D+PSGTAL + E +A A   +
Sbjct: 116 APNMSIGVNVLLKILPQLVQQLGEQYDLEMVELHHNRKKDSPSGTALRLAECLAEARGWN 175

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L D A Y REG  GER    IG  T+R GD+VG HT      GER+EITH+A SR  FA 
Sbjct: 176 LPDVANYHREGIIGERPKDEIGIQTIRGGDVVGVHTIYAMGPGERIEITHQAHSRENFAQ 235

Query: 246 GAVRSALWLSGKESG-LFDMRDVL 268
           GA+R+A WL  ++ G L+ M D+L
Sbjct: 236 GALRAAKWLPQQQPGTLYSMLDML 259


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: 195
Number of extensions: 7
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: 259
Length adjustment: 25
Effective length of query: 248
Effective length of database: 234
Effective search space:    58032
Effective search space used:    58032
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 8499684 DvMF_0450 (dihydrodipicolinate reductase (RefSeq))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.25808.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25808.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.