Alignments for a candidate for metX in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Trichormus variabilis ATCC 29413

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_011320764.1 AVA_RS20670 homoserine O-acetyltransferase

Query= SwissProt::Q3M5Q6
         (359 letters)



>NCBI__GCF_000204075.1:WP_011320764.1
          Length = 359

 Score =  725 bits (1872), Expect = 0.0
 Identities = 359/359 (100%), Positives = 359/359 (100%)

Query: 1   MNYQDFISEQTEYYHLPVPFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSAD 60
           MNYQDFISEQTEYYHLPVPFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSAD
Sbjct: 1   MNYQDFISEQTEYYHLPVPFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSAD 60

Query: 61  ADEWWEGLLGANKALDSDRDFIICSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDM 120
           ADEWWEGLLGANKALDSDRDFIICSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDM
Sbjct: 61  ADEWWEGLLGANKALDSDRDFIICSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDM 120

Query: 121 VRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLS 180
           VRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLS
Sbjct: 121 VRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLS 180

Query: 181 EAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARFGRQYDAVADQF 240
           EAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARFGRQYDAVADQF
Sbjct: 181 EAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARFGRQYDAVADQF 240

Query: 241 AIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQGRDYKSVLQSIKQPALVVAIDSDI 300
           AIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQGRDYKSVLQSIKQPALVVAIDSDI
Sbjct: 241 AIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQGRDYKSVLQSIKQPALVVAIDSDI 300

Query: 301 LYPPTEQQELADFIPDAQLGWLQSSYGHDAFLIDIATLSQLVINFRQSLSLKTFSDVTT 359
           LYPPTEQQELADFIPDAQLGWLQSSYGHDAFLIDIATLSQLVINFRQSLSLKTFSDVTT
Sbjct: 301 LYPPTEQQELADFIPDAQLGWLQSSYGHDAFLIDIATLSQLVINFRQSLSLKTFSDVTT 359


Lambda     K      H
   0.319    0.134    0.406 

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: 627
Number of extensions: 15
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: 359
Length of database: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_011320764.1 AVA_RS20670 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# 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/TIGR01392.hmm
# target sequence database:        /tmp/gapView.3881647.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-137  442.8   0.0   5.4e-137  442.5   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011320764.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011320764.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.5   0.0  5.4e-137  5.4e-137       4     349 ..      19     345 ..      17     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.5 bits;  conditional E-value: 5.4e-137
                             TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldtsryfvv 76 
                                           +++le G+vl+ v+vay+t+G+ln+++dN vl+cHaltgsa+++   +     WW+ llG ++ald +r f++
  NCBI__GCF_000204075.1:WP_011320764.1  19 PFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSADAD---E-----WWEGLLGANKALDSDRDFII 83 
                                           689****************************************9...5.....******************** PP

                             TIGR01392  77 clNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsy 149
                                           c+N lGsc+G+tg +sinp+tg pyga+fP++tirD+v+ q+al+++Lg+++l++v+GgSlGGmq+lewal y
  NCBI__GCF_000204075.1:WP_011320764.1  84 CSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDMVRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLY 156
                                           ************************************************************************* PP

                             TIGR01392 150 pervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesleerf 222
                                           pe+v++i+++ats r+sa++i+++e+qrqai++Dp++++G+y++e+ P++GLa+ARm+a+ +Yrs +s+ +rf
  NCBI__GCF_000204075.1:WP_011320764.1 157 PEIVQAIAPIATSGRHSAWCIGLSEAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARF 229
                                           ************************************************************************* PP

                             TIGR01392 223 greakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlv 295
                                           gr+  +         ++f++ syl+++g+k+v+rFdAn+Y++lt+a+d+hd+a+g   ++k++l++ik+p+lv
  NCBI__GCF_000204075.1:WP_011320764.1 230 GRQYDAV-------ADQFAIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQG--RDYKSVLQSIKQPALV 293
                                           *887776.......469*************************************9..699************* PP

                             TIGR01392 296 vgiesDllftleeqeelakalkaakleyaeieseeGHDaFllekekveeliref 349
                                           v+i+sD+l++++eq+ela+ +++a+l    ++s++GHDaFl++ +++++l+ +f
  NCBI__GCF_000204075.1:WP_011320764.1 294 VAIDSDILYPPTEQQELADFIPDAQLG--WLQSSYGHDAFLIDIATLSQLVINF 345
                                           ***************************..9******************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.25
//
[ok]

This GapMind analysis is from Jul 25 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 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