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

GapMind for Amino acid biosynthesis

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

Align homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate WP_011778808.1 MVAN_RS07820 homoserine O-acetyltransferase

Query= BRENDA::P9WJY9
         (379 letters)



>NCBI__GCF_000015305.1:WP_011778808.1
          Length = 375

 Score =  597 bits (1538), Expect = e-175
 Identities = 292/375 (77%), Positives = 326/375 (86%), Gaps = 2/375 (0%)

Query: 1   MTISDVPTQ--TLPAEGEIGLIDVGSLQLESGAVIDDVCIAVQRWGKLSPARDNVVVVLH 58
           MTI D+ T+   LP EGEI ++D+G L LE+G VIDDV IAVQRWG+LS  RDNVVVVLH
Sbjct: 1   MTIVDLLTERVALPPEGEIAIVDIGPLTLENGEVIDDVSIAVQRWGELSARRDNVVVVLH 60

Query: 59  ALTGDSHITGPAGPGHPTPGWWDGVAGPGAPIDTTRWCAVATNVLGGCRGSTGPSSLARD 118
           ALTGDSHITGPAGP HPTPGWWDGVAGPGAPIDT RWCA++TNVLGGCRGSTGPSSLA D
Sbjct: 61  ALTGDSHITGPAGPDHPTPGWWDGVAGPGAPIDTDRWCAISTNVLGGCRGSTGPSSLAPD 120

Query: 119 GKPWGSRFPLISIRDQVQADVAALAALGITEVAAVVGGSMGGARALEWVVGYPDRVRAGL 178
           GK WGSRFP ISIRDQV ADVAAL   GITEVAAV+GGSMGGARALEW++ +PD VRA L
Sbjct: 121 GKAWGSRFPTISIRDQVAADVAALERFGITEVAAVIGGSMGGARALEWMMLHPDSVRAAL 180

Query: 179 LLAVGARATADQIGTQTTQIAAIKADPDWQSGDYHETGRAPDAGLRLARRFAHLTYRGEI 238
           +LAVGARATADQIGTQ TQ+AAIK+DP+W+ GDYH TGR+PD GL +ARRFAHLTYRGE 
Sbjct: 181 VLAVGARATADQIGTQCTQVAAIKSDPNWRGGDYHGTGRSPDHGLEIARRFAHLTYRGET 240

Query: 239 ELDTRFANHNQGNEDPTAGGRYAVQSYLEHQGDKLLSRFDAGSYVILTEALNSHDVGRGR 298
           ELD RF N  Q  EDP  GGRY+VQSYLEHQG KLL+RFDAG+YV LT+AL+SHD+GRGR
Sbjct: 241 ELDERFGNDAQPGEDPATGGRYSVQSYLEHQGRKLLARFDAGTYVTLTDALSSHDIGRGR 300

Query: 299 GGVSAALRACPVPVVVGGITSDRLYPLRLQQELADLLPGCAGLRVVESVYGHDGFLVETE 358
           GGV+AAL++CPVP VVGGITSDRLYPLRLQ ELA+LLPGC GL VV+S  GHDGFLVET+
Sbjct: 301 GGVAAALQSCPVPTVVGGITSDRLYPLRLQAELAELLPGCDGLDVVDSACGHDGFLVETD 360

Query: 359 AVGELIRQTLGLADR 373
           AVG+LIR+TL LA R
Sbjct: 361 AVGKLIRRTLELAAR 375


Lambda     K      H
   0.318    0.137    0.420 

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: 524
Number of extensions: 17
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: 379
Length of database: 375
Length adjustment: 30
Effective length of query: 349
Effective length of database: 345
Effective search space:   120405
Effective search space used:   120405
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: 50 (23.9 bits)

Align candidate WP_011778808.1 MVAN_RS07820 (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.19885.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-132  426.2   0.0   5.7e-132  426.0   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011778808.1  MVAN_RS07820 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011778808.1  MVAN_RS07820 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.0   0.0  5.7e-132  5.7e-132       3     350 ..      25     370 ..      23     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 426.0 bits;  conditional E-value: 5.7e-132
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                                +ltle+Gev+++v++a++++G+l+a+rdN+v+v+Haltg++h++g a  +++  GWWd + Gpg ++d
  lcl|NCBI__GCF_000015305.1:WP_011778808.1  25 GPLTLENGEVIDDVSIAVQRWGELSARRDNVVVVLHALTGDSHITGPAGPDHPtpGWWDGVAGPGAPID 93 
                                               589*********************************************9999889************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+r++ +++NvlG+c+GstgP+s+ p+ gk +g++fP+++irD+v a+ a l+++g++++aav+GgS+G
  lcl|NCBI__GCF_000015305.1:WP_011778808.1  94 TDRWCAISTNVLGGCRGSTGPSSLAPD-GKAWGSRFPTISIRDQVAADVAALERFGITEVAAVIGGSMG 161
                                               **************************9.***************************************** PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARm 206
                                               G++alew +  p++v++++vla++ara+a++i+++ +q  ai+sDp++++G+y+ ++ +P++GL++AR+
  lcl|NCBI__GCF_000015305.1:WP_011778808.1 162 GARALEWMMLHPDSVRAALVLAVGARATADQIGTQCTQVAAIKSDPNWRGGDYHGTGrSPDHGLEIARR 230
                                               ********************************************************99*********** PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                               +a+ltYr+e++l+erfg++a+  e++a+    ++sv+syl++qg+k+++rFdA++Y++lt+al +hd++
  lcl|NCBI__GCF_000015305.1:WP_011778808.1 231 FAHLTYRGETELDERFGNDAQPGEDPAT--GGRYSVQSYLEHQGRKLLARFDAGTYVTLTDALSSHDIG 297
                                               ***********************99998..9************************************** PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakleyaeieseeGHDaFllekekvee 344
                                               rg r+++++al+++ +p++v gi+sD+l++l+ q+ela+ l+ ++    +++s+ GHD+Fl+e+++v +
  lcl|NCBI__GCF_000015305.1:WP_011778808.1 298 RG-RGGVAAALQSCPVPTVVGGITSDRLYPLRLQAELAELLPGCDGL-DVVDSACGHDGFLVETDAVGK 364
                                               **.8*****************************************99.9******************** PP

                                 TIGR01392 345 lirefl 350
                                               lir++l
  lcl|NCBI__GCF_000015305.1:WP_011778808.1 365 LIRRTL 370
                                               **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (375 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.54
//
[ok]

This GapMind analysis is from Apr 10 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