Alignments for a candidate for dapA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Shewanella amazonensis SB2B

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 6937767 Sama_1908 dihydrodipicolinate synthase (RefSeq)

Query= BRENDA::A5F699
         (292 letters)



>FitnessBrowser__SB2B:6937767
          Length = 293

 Score =  344 bits (882), Expect = 2e-99
 Identities = 169/289 (58%), Positives = 217/289 (75%)

Query: 1   MFSGSIVALITPFTPDGEVDYISLKKLVDFHVDAGTDAIVSVGTTGESATLTVEEHVKVV 60
           M +GSIVALITP   DG VD+ SL+ LV+FH+  GTDAIV+VGTTGESATL ++EH+ VV
Sbjct: 1   MINGSIVALITPMNSDGSVDFASLESLVEFHIANGTDAIVAVGTTGESATLPMKEHINVV 60

Query: 61  AKTVEFAEGRLPIIAGTGANATHEAVTFSRLLNNTGIAGYLSVTPYYNKPTQEGLFLHYN 120
           AKTVEFA+GR+P+I G GANAT EA+  ++ L+ TG+A  L VTPYYNKPT +GL  HY 
Sbjct: 61  AKTVEFAKGRIPVIGGNGANATAEAIELTQALSATGVAAMLGVTPYYNKPTPKGLVAHYK 120

Query: 121 AIAQETDIPVILYNVPGRTAVDMRPETVARLSEIKNIVALKDATGDLSRVAKHREMCKEG 180
           A+A  TDIP ILYNVPGRTA+D++PETVA L ++ NI+ +K+ATGD+SRVA+ RE+C   
Sbjct: 121 AVAAATDIPQILYNVPGRTALDLKPETVAELCDVANIIGIKEATGDVSRVARLRELCGPD 180

Query: 181 FVLLSGDDATGLEFVKLGGQGVISVTNNIAAADMAKMMHLALDGKFDEAASINQRLMTLH 240
           F+L SGDDAT  EF+  GG GVISV NNI  A   KM  LAL G  + + + ++ +  L+
Sbjct: 181 FLLYSGDDATAREFLLAGGDGVISVANNIVPAQFKKMCALALAGDIEGSLAADEPMRGLY 240

Query: 241 KNLFIESSPIPVKWAAHKMGLIANGDLRLPLTQLSEPARPIVAQALSEA 289
             LF E++PIPVKWAAH+MGLI  G +RLPLT+LSE    ++  A+ +A
Sbjct: 241 STLFCEANPIPVKWAAHRMGLIKEGFIRLPLTELSESCHGLLLDAMKKA 289


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: 327
Number of extensions: 8
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: 293
Length adjustment: 26
Effective length of query: 266
Effective length of database: 267
Effective search space:    71022
Effective search space used:    71022
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 6937767 Sama_1908 (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.6087.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-110  354.0   0.0   2.5e-110  353.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937767  Sama_1908 dihydrodipicolinate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937767  Sama_1908 dihydrodipicolinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.8   0.0  2.5e-110  2.5e-110       1     284 [.       4     287 ..       4     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 353.8 bits;  conditional E-value: 2.5e-110
                         TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsn 77 
                                       g+++AliTP+++dgsvdfa+le+l+e++i++g+daiv+vGtTGEsatL ++E+++v+ ++ve++k+r+pvi G g+n
  lcl|FitnessBrowser__SB2B:6937767   4 GSIVALITPMNSDGSVDFASLESLVEFHIANGTDAIVAVGTTGESATLPMKEHINVVAKTVEFAKGRIPVIGGNGAN 80 
                                       589************************************************************************** PP

                         TIGR00674  78 ateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeevei 154
                                       at+eaielt+ ++ +gv+++l vtPyYnkPt +Gl++h+ka+a+++++P+ilYnvP+Rt+ +l+petv++L +  +i
  lcl|FitnessBrowser__SB2B:6937767  81 ATAEAIELTQALSATGVAAMLGVTPYYNKPTPKGLVAHYKAVAAATDIPQILYNVPGRTALDLKPETVAELCDVANI 157
                                       ***************************************************************************** PP

                         TIGR00674 155 vaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihq 231
                                       ++iKea+gd++rv ++++  + df ++sGdDa++ e+l+ G+ GviSVa+n++p ++k+m++ al+gd+e  +  ++
  lcl|FitnessBrowser__SB2B:6937767 158 IGIKEATGDVSRVARLRELCGPDFLLYSGDDATAREFLLAGGDGVISVANNIVPAQFKKMCALALAGDIEGSLAADE 234
                                       ***************************************************************************** PP

                         TIGR00674 232 kllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284
                                        +  l+++lf+e+NPipvK+a++ +gli++  +RlPLtelse+ +  l +++k
  lcl|FitnessBrowser__SB2B:6937767 235 PMRGLYSTLFCEANPIPVKWAAHRMGLIKEGFIRLPLTELSESCHGLLLDAMK 287
                                       ******************************************98877777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (293 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.97
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis