GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Shewanella loihica PV-4

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 5209914 Shew_2362 dihydrodipicolinate synthase (RefSeq)

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__PV4:5209914
          Length = 304

 Score =  150 bits (380), Expect = 3e-41
 Identities = 90/287 (31%), Positives = 159/287 (55%), Gaps = 4/287 (1%)

Query: 2   FKGVYPAIITPFKNK-EVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIE 60
           ++GV+PAI T F +   ++++     +  LI +G+ G++A+GT GE+ +LS EE ++ I+
Sbjct: 5   WQGVFPAISTQFNDDGSINYESNARMLEDLIRDGIDGVIALGTIGENASLSPEEKREFIK 64

Query: 61  KVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGK 120
             V+ VNGR+ V++G   N  ++A + +   E +G D ++ +     + T   +  H+  
Sbjct: 65  HTVETVNGRILVLSGCTENTAQQAAKYAQDVEALGVDGLMLLPAMVYRGTDREVIAHYQH 124

Query: 121 VAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSEL--IHDAK 178
           VA S  LPI++YN P    V++  +   +LAEE  NI A+KE+  +  +++EL      +
Sbjct: 125 VARSTKLPIMIYNNPVGYGVDINLEMTAVLAEE-PNIVAIKESTTDTRRLTELQSRFGDR 183

Query: 179 ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLM 238
             +L G D++ L  I LG  G IS + N+ P+E V +   A  G  E+AREI+    PL+
Sbjct: 184 FNILCGVDDIALESILLGATGWISGLTNVFPRESVTLFKLARAGRIEEAREIYRWFMPLL 243

Query: 239 KAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKD 285
           +   I T    +K A  ++GR +  +RLP   +  + +  +E V+ +
Sbjct: 244 RLDTIPTLVQCIKFAEQIVGRGSENVRLPRMTLIGDERAYVEKVMAE 290


Lambda     K      H
   0.315    0.135    0.374 

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: 215
Number of extensions: 9
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: 289
Length of database: 304
Length adjustment: 26
Effective length of query: 263
Effective length of database: 278
Effective search space:    73114
Effective search space used:    73114
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate 5209914 Shew_2362 (dihydrodipicolinate synthase (RefSeq))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.4509.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4509.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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