GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas putida KT2440

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate PP_2639 PP_2639 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__Putida:PP_2639
          Length = 288

 Score =  166 bits (421), Expect = 4e-46
 Identities = 99/287 (34%), Positives = 156/287 (54%), Gaps = 4/287 (1%)

Query: 2   FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61
           F+G++ A++TP +  E+DF GLE+ +  L+E+GV+G V  GTTGE+  LS  E   V++ 
Sbjct: 4   FRGIWIALVTPMRANEIDFPGLEKLVKKLLEDGVAGFVVCGTTGEAAALSKAEQLAVLDA 63

Query: 62  VVDVVNGRVQVIAGAGSNCTEE-AIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGK 120
           V+  V     V+  +G N  E  A +  +   D+G   +L   P Y +P+Q G+   F  
Sbjct: 64  VLAWVEPGRMVMGLSGYNLRELLAFQAEIQQRDIGG--LLVPAPCYIRPSQAGIEAFFAT 121

Query: 121 VAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAKIT 180
           VA++ ++P+++Y++P RT V +E +T++ +   +  I+AVK+   +      LI D    
Sbjct: 122 VADAASVPVIVYDIPYRTGVRIERETLRRIVR-HPRIAAVKDCGGDSETTMALIEDGHAQ 180

Query: 181 VLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKA 240
           VL+G D      + LGG G IS  A++    +V MV     GD+  AR   Y+L P +K 
Sbjct: 181 VLAGEDLQIFNNLCLGGAGAISASAHVRADLYVRMVRQVDSGDWAAARGTFYQLLPWIKV 240

Query: 241 MFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDLG 287
            F E NP  VK AL +    A ELR P+   +   +  L++VL  LG
Sbjct: 241 AFAEPNPAVVKAALQLQSLIADELREPMQTCTNTTRDKLQSVLCSLG 287


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: 159
Number of extensions: 6
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: 288
Length adjustment: 26
Effective length of query: 263
Effective length of database: 262
Effective search space:    68906
Effective search space used:    68906
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 PP_2639 PP_2639 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.17042.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17042.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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