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

GapMind for Amino acid biosynthesis

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

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 5209377 Shew_1848 dihydrodipicolinate synthase (RefSeq)

Query= BRENDA::A5F699
         (292 letters)



>FitnessBrowser__PV4:5209377
          Length = 294

 Score =  338 bits (867), Expect = 9e-98
 Identities = 169/291 (58%), Positives = 213/291 (73%)

Query: 1   MFSGSIVALITPFTPDGEVDYISLKKLVDFHVDAGTDAIVSVGTTGESATLTVEEHVKVV 60
           M +GSIVALITP   DG VDY SL+KLV++H++ GTDAIV+VGTTGESATL + EH++VV
Sbjct: 1   MINGSIVALITPMNRDGSVDYASLEKLVEYHIEQGTDAIVAVGTTGESATLPLSEHIEVV 60

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

Query: 121 AIAQETDIPVILYNVPGRTAVDMRPETVARLSEIKNIVALKDATGDLSRVAKHREMCKEG 180
           A+A  TDIP ILYNVPGRT+VDM PETVA+L ++ NI+ +K+ATGDLSRVA+ RE+C + 
Sbjct: 121 AVAAATDIPQILYNVPGRTSVDMLPETVAQLVDVPNIIGVKEATGDLSRVARLRELCGDD 180

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

Query: 241 KNLFIESSPIPVKWAAHKMGLIANGDLRLPLTQLSEPARPIVAQALSEACI 291
             LF E++PIPVKWAAH+MGLI+ G +RLPLT+LSE    ++ +A+  A I
Sbjct: 241 SALFCEANPIPVKWAAHRMGLISQGHIRLPLTELSEQYHGLLLEAMKNAGI 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: 286
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: 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 5209377 Shew_1848 (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.7292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   8.9e-114  365.1   0.0   9.9e-114  365.0   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209377  Shew_1848 dihydrodipicolinate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209377  Shew_1848 dihydrodipicolinate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.0   0.0  9.9e-114  9.9e-114       1     284 [.       4     287 ..       4     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 365.0 bits;  conditional E-value: 9.9e-114
                        TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsna 78 
                                      g+++AliTP+++dgsvd+a+lekl+e++ie+g+daiv+vGtTGEsatL l E+++v+  +v+++++rvpvi G g+na
  lcl|FitnessBrowser__PV4:5209377   4 GSIVALITPMNRDGSVDYASLEKLVEYHIEQGTDAIVAVGTTGESATLPLSEHIEVVAHTVKFAAGRVPVIGGNGANA 81 
                                      589*************************************************************************** PP

                        TIGR00674  79 teeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeveiva 156
                                      t+eaieltk  ++lgv+++l vtPyYnkPt +Gl++h+ a+a+++++P+ilYnvP+Rt+v++ petv++L++ ++i++
  lcl|FitnessBrowser__PV4:5209377  82 TAEAIELTKAQANLGVAAMLGVTPYYNKPTPKGLVAHYSAVAAATDIPQILYNVPGRTSVDMLPETVAQLVDVPNIIG 159
                                      ****************************************************************************** PP

                        TIGR00674 157 iKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihqkll 234
                                      +Kea+gdl+rv ++++  ++df ++sGdDa++ e+l+lG++GviSVa+n++pk++k m+ aal+gd e a++ ++ ++
  lcl|FitnessBrowser__PV4:5209377 160 VKEATGDLSRVARLRELCGDDFMLYSGDDATAREFLTLGGNGVISVANNIVPKQFKLMCDAALKGDLEGALKAEAPMK 237
                                      ****************************************************************************** PP

                        TIGR00674 235 klfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284
                                      +lf+alf+e+NPipvK+a++ +gli + ++RlPLtelse+ +  l e++k
  lcl|FitnessBrowser__PV4:5209377 238 DLFSALFCEANPIPVKWAAHRMGLISQGHIRLPLTELSEQYHGLLLEAMK 287
                                      ***************************************98877766665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.27
//
[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