Alignments for a candidate for metA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Shewanella amazonensis SB2B

Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate 6937204 Sama_1374 homoserine O-succinyltransferase (RefSeq)

Query= SwissProt::A6WLE9
         (313 letters)



>FitnessBrowser__SB2B:6937204
          Length = 316

 Score =  557 bits (1435), Expect = e-163
 Identities = 259/312 (83%), Positives = 290/312 (92%)

Query: 1   MPVRIPDHLPAAEVLESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60
           MPV+IPD+LPAAE+L +ENIFVMSETRAA+QDIRPMKVLILNLMPNKIETETQLLRLLGN
Sbjct: 1   MPVKIPDNLPAAEILSAENIFVMSETRAAHQDIRPMKVLILNLMPNKIETETQLLRLLGN 60

Query: 61  TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEAVRHKNYDGLIITGAPLGQIDFEDVVY 120
           TPLQVDVDLLRIHDKES+HTS+DHMNTFYRDFE VRHKNYDGLIITGAPLGQ+DFE+V Y
Sbjct: 61  TPLQVDVDLLRIHDKESRHTSLDHMNTFYRDFEDVRHKNYDGLIITGAPLGQLDFEEVTY 120

Query: 121 WDHIREIIDWSQEHVTSVLFLCWAAHAGLYHLYGLNRKILQQKRSGVFVHRRTSQHFPLL 180
           WDHIREIIDWSQ HVTSVLFLCWAAHAGLYHLYGL R++L+ KRSGVFVH R+  H PLL
Sbjct: 121 WDHIREIIDWSQSHVTSVLFLCWAAHAGLYHLYGLKRELLKTKRSGVFVHSRSCDHHPLL 180

Query: 181 RGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPEYQK 240
           RGFD+EFFAPHSR+AE+ V +I  HP LQ+LAESDEAGAYLVLSRN+RNLFV+GHPEYQK
Sbjct: 181 RGFDEEFFAPHSRYAEIPVAQIHAHPALQVLAESDEAGAYLVLSRNSRNLFVIGHPEYQK 240

Query: 241 STLNEEYQRDLSQGLDPNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYD 300
           STL++EY RDL+ G++P +PQNY+RNDDP    +ARWHSHGSLLVSNWLNYYVYQLTPYD
Sbjct: 241 STLSDEYHRDLAAGINPEIPQNYFRNDDPAQPPVARWHSHGSLLVSNWLNYYVYQLTPYD 300

Query: 301 LSDMTAMTPWES 312
           LSDM+A+TPWE+
Sbjct: 301 LSDMSAITPWEA 312


Lambda     K      H
   0.321    0.136    0.419 

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: 470
Number of extensions: 10
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: 313
Length of database: 316
Length adjustment: 27
Effective length of query: 286
Effective length of database: 289
Effective search space:    82654
Effective search space used:    82654
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 6937204 Sama_1374 (homoserine O-succinyltransferase (RefSeq))
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))

# 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/TIGR01001.hmm
# target sequence database:        /tmp/gapView.12772.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01001  [M=301]
Accession:   TIGR01001
Description: metA: homoserine O-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.9e-143  463.5   0.1   2.2e-143  463.3   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6937204  Sama_1374 homoserine O-succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937204  Sama_1374 homoserine O-succinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.3   0.1  2.2e-143  2.2e-143       1     300 [.       1     301 [.       1     302 [. 0.99

  Alignments for each domain:
  == domain 1  score: 463.3 bits;  conditional E-value: 2.2e-143
                         TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrks 77 
                                       mp+++pd+lpa e+l  enifvm+e ra hqdirp++vlilnlmp+kiete+qllrll+n+plqvd++llri++++s
  lcl|FitnessBrowser__SB2B:6937204   1 MPVKIPDNLPAAEILSAENIFVMSETRAAHQDIRPMKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKES 77 
                                       9**************************************************************************** PP

                         TIGR01001  78 kntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkllyg 154
                                       ++t  +h+++fy+++e+v+++++dGli+tGap+++l+fe+v yw++++ei++ws+++vts l++cwaa+a+l+ lyg
  lcl|FitnessBrowser__SB2B:6937204  78 RHTSLDHMNTFYRDFEDVRHKNYDGLIITGAPLGQLDFEEVTYWDHIREIIDWSQSHVTSVLFLCWAAHAGLYHLYG 154
                                       ***************************************************************************** PP

                         TIGR01001 155 ipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskdernif 230
                                       +++  l+ k sGv+ h+   ++++llrgfd++f+aphsrya+++ ++i++++ l++laesdeag+yl++s++ rn+f
  lcl|FitnessBrowser__SB2B:6937204 155 LKRELLKTKRSGVFVHSRScDHHPLLRGFDEEFFAPHSRYAEIPVAQIHAHPALQVLAESDEAGAYLVLSRNSRNLF 231
                                       ****************99889******************************************************** PP

                         TIGR01001 231 vtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydl 300
                                       v+Ghpey+k tl +ey rd+ +g++++ip+ny+ +ddp + p+a w+sh+ ll +nwlny+vyq tpydl
  lcl|FitnessBrowser__SB2B:6937204 232 VIGHPEYQKSTLSDEYHRDLAAGINPEIPQNYFRNDDPAQPPVARWHSHGSLLVSNWLNYYVYQLTPYDL 301
                                       ********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (316 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: 10.03
//
[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