Alignments for a candidate for dapD in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Amycolatopsis halophila YIM 93223

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate WP_034275067.1 AMYHA_RS24955 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= BRENDA::P9WP21
         (317 letters)



>NCBI__GCF_000504245.1:WP_034275067.1
          Length = 333

 Score =  422 bits (1084), Expect = e-123
 Identities = 211/322 (65%), Positives = 250/322 (77%), Gaps = 10/322 (3%)

Query: 5   TGAAGIGLATLAADGSVLDTWFPAPELTESGTSA-----TSRLAVSDVPVELA----ALI 55
           TGA G+GLAT+  DG+VLDTWFP P+LT +   A     T++L+  +    L      L+
Sbjct: 12  TGATGVGLATITTDGTVLDTWFPHPKLTSTSGQAGEQAGTTKLSDDEAAAALGKAATTLL 71

Query: 56  GRDDDRRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVV 115
           G D DR  E IAVRT IGSL     D +D YLRLHLLSHR+V PHG N  G+FG+L+NVV
Sbjct: 72  GSDTDRGVEVIAVRTTIGSLSTAPQDAHDVYLRLHLLSHRMVRPHGQNMNGVFGLLSNVV 131

Query: 116 WTNHGPCAIDGFEAVRARLRRRGPVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLA 175
           WTN GPC ++GFEA R RLR RG VTVY +DKFPRMVDYV+P+GVRI DADRVRLGAHLA
Sbjct: 132 WTNFGPCPVEGFEATRMRLRSRGHVTVYSIDKFPRMVDYVIPSGVRIGDADRVRLGAHLA 191

Query: 176 PGTTVMHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIG 235
            GTTVMHEGF+N+NAGTLGASM+EGRISAGVVVGDG+D+GG AS+MGTLSGGG  VIS+G
Sbjct: 192 SGTTVMHEGFINFNAGTLGASMIEGRISAGVVVGDGTDLGGSASVMGTLSGGGKEVISVG 251

Query: 236 KRCLLGANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVS 295
           +RCLLGAN+G+GISLGDD VVEAGLYVTAGT+V++ +    KA +LSG S  LFRRNS +
Sbjct: 252 ERCLLGANAGIGISLGDDSVVEAGLYVTAGTKVSV-EGTLRKASDLSGISGALFRRNSAT 310

Query: 296 GAVEVLARDGQGIALNEDLHAN 317
           G VE + R+G GI LN +LH N
Sbjct: 311 GVVEAVRREGTGIELNAELHKN 332


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: 392
Number of extensions: 18
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: 317
Length of database: 333
Length adjustment: 28
Effective length of query: 289
Effective length of database: 305
Effective search space:    88145
Effective search space used:    88145
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_034275067.1 AMYHA_RS24955 (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.3404074.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-154  498.6  12.3   3.8e-154  498.4  12.3    1.0  1  NCBI__GCF_000504245.1:WP_034275067.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034275067.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.4  12.3  3.8e-154  3.8e-154       2     320 .]      13     332 ..      12     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 498.4 bits;  conditional E-value: 3.8e-154
                             TIGR03535   2 salglGlatvtadgtvldvWypelelgea.....aeagterleae......leelaa....lagedeargver 59 
                                           +a+g+Glat+t+dgtvld+W+p+++l+++     ++agt++l+ +           +    l+g+d +rgve+
  NCBI__GCF_000504245.1:WP_034275067.1  13 GATGVGLATITTDGTVLDTWFPHPKLTSTsgqagEQAGTTKLSDDeaaaalG----KaattLLGSDTDRGVEV 81 
                                           799***********************98865555566666666655633332....2444599********** PP

                             TIGR03535  60 vvvttkiadldeapadaadaylrlhllshrlvkPntvnldGifgllanvvWtnlGPvavedlektraklraeg 132
                                            +v+t+i++l++ap+da+d+ylrlhllshr+v+P+++n++G+fgll+nvvWtn+GP+ ve++e+tr++lr +g
  NCBI__GCF_000504245.1:WP_034275067.1  82 IAVRTTIGSLSTAPQDAHDVYLRLHLLSHRMVRPHGQNMNGVFGLLSNVVWTNFGPCPVEGFEATRMRLRSRG 154
                                           ************************************************************************* PP

                             TIGR03535 133 pvtvysvdkfPrmvdyvvPtgvrigdadrvrlGaylaeGttvmheGfvnfnaGtlGasmveGrisaGvvvgdG 205
                                           +vtvys+dkfPrmvdyv+P+gvrigdadrvrlGa+la+GttvmheGf+nfnaGtlGasm+eGrisaGvvvgdG
  NCBI__GCF_000504245.1:WP_034275067.1 155 HVTVYSIDKFPRMVDYVIPSGVRIGDADRVRLGAHLASGTTVMHEGFINFNAGTLGASMIEGRISAGVVVGDG 227
                                           ************************************************************************* PP

                             TIGR03535 206 sdiGGGasimGtlsGGGkevisiGercllGansGvGislGddcvveaGlyvtaGtkvtlvdkakeaageegev 278
                                           +d+GG as+mGtlsGGGkevis+GercllGan+G+GislGdd+vveaGlyvtaGtkv++          eg++
  NCBI__GCF_000504245.1:WP_034275067.1 228 TDLGGSASVMGTLSGGGKEVISVGERCLLGANAGIGISLGDDSVVEAGLYVTAGTKVSV----------EGTL 290
                                           ***********************************************************..........899* PP

                             TIGR03535 279 vkaaelsGasnllfrrnsvsGaveavarkgkaielnealhan 320
                                            ka++lsG s+ lfrrns++G veav+r+g++ieln++lh+n
  NCBI__GCF_000504245.1:WP_034275067.1 291 RKASDLSGISGALFRRNSATGVVEAVRREGTGIELNAELHKN 332
                                           ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (320 nodes)
Target sequences:                          1  (333 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: 20.20
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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