GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas simiae WCS417

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate GFF2865 PS417_14640 dihydrodipicolinate synthase

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__WCS417:GFF2865
          Length = 287

 Score =  153 bits (387), Expect = 4e-42
 Identities = 94/285 (32%), Positives = 146/285 (51%), Gaps = 8/285 (2%)

Query: 2   FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61
           F+G++  ++TPF +  +DF GL   ++ L+E  V+GI+   TTGE+  LS +E   V++ 
Sbjct: 4   FQGIWVPVVTPFHDGAIDFTGLHRLVSHLLEKHVAGIMVCTTTGEAAALSRQEQLAVLDA 63

Query: 62  VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSI---TPYYNKPTQEGLRKHF 118
           V+  V     V+  AG N     IEL  F  ++    V  +    P Y +P+Q GL   F
Sbjct: 64  VLQWVPAHRVVMGLAGYN----QIELLQFQREILQRPVAGLLVPAPSYIRPSQAGLEAFF 119

Query: 119 GKVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK 178
             VA++ ++PI+LY++P RT    E  T+ L    +  I A+K+   NL     L+    
Sbjct: 120 RTVADASSVPIILYDIPYRTGATFEQATL-LNIVAHERIVAIKDCGGNLGNTLALLASGD 178

Query: 179 ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLM 238
           + VL G D      + LG  G I+  A++  ++FV +     +    +AR   ++L PL+
Sbjct: 179 VEVLCGEDVQIFNALCLGATGAIAASAHLQTEQFVALCQLVRDNQLAEARATFFELLPLI 238

Query: 239 KAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVL 283
            AMF+E NP PVK AL + G    ELR P+   S      L+ VL
Sbjct: 239 NAMFMEPNPAPVKAALALQGLIGSELRAPMQAASTAVVARLQQVL 283


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: 192
Number of extensions: 8
Number of successful extensions: 3
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: 287
Length adjustment: 26
Effective length of query: 263
Effective length of database: 261
Effective search space:    68643
Effective search space used:    68643
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: 47 (22.7 bits)

Align candidate GFF2865 PS417_14640 (dihydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.30987.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30987.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.