GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Shewanella sp. ANA-3

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 7024478 Shewana3_1656 dihydrodipicolinate synthase (RefSeq)

Query= BRENDA::A5F699
         (292 letters)



>FitnessBrowser__ANA3:7024478
          Length = 294

 Score =  344 bits (883), Expect = 1e-99
 Identities = 173/291 (59%), Positives = 215/291 (73%)

Query: 1   MFSGSIVALITPFTPDGEVDYISLKKLVDFHVDAGTDAIVSVGTTGESATLTVEEHVKVV 60
           M +GSIVALITP   DG VD+ SL++LV+FH+D GTDAIV+VGTTGESATL + EHV VV
Sbjct: 1   MINGSIVALITPMNSDGSVDFASLERLVEFHIDQGTDAIVAVGTTGESATLPMNEHVTVV 60

Query: 61  AKTVEFAEGRLPIIAGTGANATHEAVTFSRLLNNTGIAGYLSVTPYYNKPTQEGLFLHYN 120
           A+TV+FA GR+P+I G GANAT EA+  ++ L+  G+A  L VTPYYNKPT +GL  HY 
Sbjct: 61  AQTVKFAAGRIPVIGGNGANATSEAIELTKSLSKVGVAAMLGVTPYYNKPTPKGLVAHYK 120

Query: 121 AIAQETDIPVILYNVPGRTAVDMRPETVARLSEIKNIVALKDATGDLSRVAKHREMCKEG 180
           A+A  TDIP ILYNVPGRTAVDM+PETVA L  + NI+ +K+ATGD+SRV + RE+C   
Sbjct: 121 AVAASTDIPQILYNVPGRTAVDMKPETVAELVAVSNIIGVKEATGDVSRVQRLRELCGND 180

Query: 181 FVLLSGDDATGLEFVKLGGQGVISVTNNIAAADMAKMMHLALDGKFDEAASINQRLMTLH 240
           F+L SGDDAT  EF+ LGG GVISV NNI       M   AL G  + AASI++ L  L+
Sbjct: 181 FMLYSGDDATAREFLLLGGNGVISVANNIVPKAFKAMCDAALAGNAELAASIDEPLRGLY 240

Query: 241 KNLFIESSPIPVKWAAHKMGLIANGDLRLPLTQLSEPARPIVAQALSEACI 291
             LF E++PIPVKWAAH+MGLI  G +RLPLT+LSE    ++  A++ A I
Sbjct: 241 STLFCEANPIPVKWAAHRMGLIECGHIRLPLTELSEQCHGLLLDAMTRAQI 291


Lambda     K      H
   0.318    0.134    0.379 

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: 279
Number of extensions: 5
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: 292
Length of database: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 7024478 Shewana3_1656 (dihydrodipicolinate synthase (RefSeq))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00674.hmm
# target sequence database:        /tmp/gapView.3690826.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.1e-115  369.2   0.1   5.8e-115  369.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7024478  Shewana3_1656 dihydrodipicolinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024478  Shewana3_1656 dihydrodipicolinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.0   0.1  5.8e-115  5.8e-115       1     281 [.       4     284 ..       4     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 369.0 bits;  conditional E-value: 5.8e-115
                         TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsn 77 
                                       g+++AliTP+++dgsvdfa+le+l+e++i++g+daiv+vGtTGEsatL ++E+++v+  +v+++++r+pvi G g+n
  lcl|FitnessBrowser__ANA3:7024478   4 GSIVALITPMNSDGSVDFASLERLVEFHIDQGTDAIVAVGTTGESATLPMNEHVTVVAQTVKFAAGRIPVIGGNGAN 80 
                                       589************************************************************************** PP

                         TIGR00674  78 ateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeevei 154
                                       at+eaieltk ++k+gv+++l vtPyYnkPt +Gl++h+ka+a+++++P+ilYnvP+Rt+v+++petv++L++  +i
  lcl|FitnessBrowser__ANA3:7024478  81 ATSEAIELTKSLSKVGVAAMLGVTPYYNKPTPKGLVAHYKAVAASTDIPQILYNVPGRTAVDMKPETVAELVAVSNI 157
                                       ***************************************************************************** PP

                         TIGR00674 155 vaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihq 231
                                       +++Kea+gd++rv+++++  ++df ++sGdDa++ e+l+lG++GviSVa+n++pk +k m+ aal+g+ e a+ i++
  lcl|FitnessBrowser__ANA3:7024478 158 IGVKEATGDVSRVQRLRELCGNDFMLYSGDDATAREFLLLGGNGVISVANNIVPKAFKAMCDAALAGNAELAASIDE 234
                                       ***************************************************************************** PP

                         TIGR00674 232 kllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklke 281
                                        l  l+++lf+e+NPipvK+a++ +glie+ ++RlPLtelse+ +  l +
  lcl|FitnessBrowser__ANA3:7024478 235 PLRGLYSTLFCEANPIPVKWAAHRMGLIECGHIRLPLTELSEQCHGLLLD 284
                                       *****************************************997766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (294 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.18
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory