Alignments for a candidate for dapD in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Mycolicibacterium vanbaalenii PYR-1

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate WP_011781671.1 MVAN_RS22700 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= BRENDA::P9WP21
         (317 letters)



>NCBI__GCF_000015305.1:WP_011781671.1
          Length = 318

 Score =  520 bits (1338), Expect = e-152
 Identities = 258/318 (81%), Positives = 287/318 (90%), Gaps = 4/318 (1%)

Query: 4   VTGAAGIGLATLAADGSVLDTWFPAPELTESGTSATSRLAVSDVPVELAALIGRDDDRRT 63
           +T A+GIG+AT+AADGSVLDTWFPAPELT+ G + T RL+V++VP ELAAL GRD+DR  
Sbjct: 1   MTSASGIGVATIAADGSVLDTWFPAPELTDGGEAGTVRLSVAEVPAELAALAGRDEDRDV 60

Query: 64  ETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWTNHGPCA 123
           + + VRTVI SLDD A D YDAYLRLHLLSHRLVAPHGLNA GLFGVLTNVVWT+HGPCA
Sbjct: 61  DVVVVRTVIASLDDKAVDAYDAYLRLHLLSHRLVAPHGLNADGLFGVLTNVVWTSHGPCA 120

Query: 124 IDGFEAVRARLRRRGPVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAPGTTVMHE 183
           +DGFE VRARLRRRG V VYGVDKFPRMVDYV+P+GVRIADADRVRLGAHLAPGTTVMHE
Sbjct: 121 VDGFETVRARLRRRGHVAVYGVDKFPRMVDYVLPSGVRIADADRVRLGAHLAPGTTVMHE 180

Query: 184 GFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGKRCLLGAN 243
           GFVN+NAGTLG+SMVEGRISAGVVV DGSDVGGGASIMGTLSGGGT VIS+GKRCLLGAN
Sbjct: 181 GFVNFNAGTLGSSMVEGRISAGVVVDDGSDVGGGASIMGTLSGGGTQVISVGKRCLLGAN 240

Query: 244 SGLGISLGDDCVVEAGLYVTAGTRVTMPD----SNSVKARELSGSSNLLFRRNSVSGAVE 299
           +GLGISLGDDCV+EAGLYVTAGT+VT+ D    + +VKARELSG++NLLFRRNSV+GAVE
Sbjct: 241 AGLGISLGDDCVIEAGLYVTAGTKVTLLDGDRTATTVKARELSGANNLLFRRNSVTGAVE 300

Query: 300 VLARDGQGIALNEDLHAN 317
           V+ RDG GI LNE LHAN
Sbjct: 301 VVKRDGTGITLNEALHAN 318


Lambda     K      H
   0.318    0.136    0.397 

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: 414
Number of extensions: 17
Number of successful extensions: 2
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: 317
Length of database: 318
Length adjustment: 27
Effective length of query: 290
Effective length of database: 291
Effective search space:    84390
Effective search space used:    84390
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 WP_011781671.1 MVAN_RS22700 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR03535 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR03535.hmm
# target sequence database:        /tmp/gapView.26347.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03535  [M=320]
Accession:   TIGR03535
Description: DapD_actino: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-165  534.3  13.0   5.1e-165  534.2  13.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011781671.1  MVAN_RS22700 2,3,4,5-tetrahydrop


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011781671.1  MVAN_RS22700 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.2  13.0  5.1e-165  5.1e-165       1     320 []       2     318 .]       2     318 .] 0.98

  Alignments for each domain:
  == domain 1  score: 534.2 bits;  conditional E-value: 5.1e-165
                                 TIGR03535   1 rsalglGlatvtadgtvldvWypelelgeaaeagterleae..leelaalagedeargvervvvttkia 67 
                                               +sa g+G+at++adg+vld+W+p++el++  eagt rl+++  ++elaalag+de+r+v++vvv+t+ia
  lcl|NCBI__GCF_000015305.1:WP_011781671.1   2 TSASGIGVATIAADGSVLDTWFPAPELTDGGEAGTVRLSVAevPAELAALAGRDEDRDVDVVVVRTVIA 70 
                                               589*********************************99987789************************* PP

                                 TIGR03535  68 dldeapadaadaylrlhllshrlvkPntvnldGifgllanvvWtnlGPvavedlektraklraegpvtv 136
                                               +ld++++da+daylrlhllshrlv P+++n dG+fg+l+nvvWt++GP+av+++e++ra+lr++g+v v
  lcl|NCBI__GCF_000015305.1:WP_011781671.1  71 SLDDKAVDAYDAYLRLHLLSHRLVAPHGLNADGLFGVLTNVVWTSHGPCAVDGFETVRARLRRRGHVAV 139
                                               ********************************************************************* PP

                                 TIGR03535 137 ysvdkfPrmvdyvvPtgvrigdadrvrlGaylaeGttvmheGfvnfnaGtlGasmveGrisaGvvvgdG 205
                                               y+vdkfPrmvdyv+P+gvri+dadrvrlGa+la GttvmheGfvnfnaGtlG+smveGrisaGvvv+dG
  lcl|NCBI__GCF_000015305.1:WP_011781671.1 140 YGVDKFPRMVDYVLPSGVRIADADRVRLGAHLAPGTTVMHEGFVNFNAGTLGSSMVEGRISAGVVVDDG 208
                                               ********************************************************************* PP

                                 TIGR03535 206 sdiGGGasimGtlsGGGkevisiGercllGansGvGislGddcvveaGlyvtaGtkvtlvdkakeaag. 273
                                               sd+GGGasimGtlsGGG++vis+G+rcllGan+G+GislGddcv+eaGlyvtaGtkvtl+d      g 
  lcl|NCBI__GCF_000015305.1:WP_011781671.1 209 SDVGGGASIMGTLSGGGTQVISVGKRCLLGANAGLGISLGDDCVIEAGLYVTAGTKVTLLD------Gd 271
                                               ***********************************************************44......43 PP

                                 TIGR03535 274 eegevvkaaelsGasnllfrrnsvsGaveavarkgkaielnealhan 320
                                               +++++vka+elsGa+nllfrrnsv+Gave+v+r+g++i+lnealhan
  lcl|NCBI__GCF_000015305.1:WP_011781671.1 272 RTATTVKARELSGANNLLFRRNSVTGAVEVVKRDGTGITLNEALHAN 318
                                               56789****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (320 nodes)
Target sequences:                          1  (318 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: 7.09
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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