Alignments for a candidate for metA in Thermophagus xiamenensis HS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metA in Thermophagus xiamenensis HS1

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_010526168.1 GQW_RS0100790 homoserine O-succinyltransferase

Query= SwissProt::Q72X44
         (301 letters)



>NCBI__GCF_000220155.1:WP_010526168.1
          Length = 302

 Score =  374 bits (960), Expect = e-108
 Identities = 175/299 (58%), Positives = 231/299 (77%)

Query: 1   MPIIIDKDLPARKVLQEENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGN 60
           MP+ I   LPA+ +L+ EN+FVM + RA TQDIR L+I ILNLMP K +TE  LLR++ N
Sbjct: 1   MPVNIPDLLPAKSLLEAENVFVMGESRAVTQDIRPLRILILNLMPLKIKTETHLLRVLSN 60

Query: 61  TPLQLDVHLLHMESHLSRNVAQEHLTSFYKTFRDIENEKFDGLIITGAPVETLSFEEVDY 120
           TPLQ++V LL   +H  +N   +HL SFYKTF +I+ + +DG IITGAPVE L FE+V Y
Sbjct: 61  TPLQVEVELLITSTHTPKNTPSQHLISFYKTFDEIKGKNYDGFIITGAPVELLDFEKVTY 120

Query: 121 WEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQHVKLL 180
           W EL++IM++SKT+VTSTLHICWGAQAGLYHHYG+ K+ L  K+FGVFEH V +    L+
Sbjct: 121 WNELQKIMDWSKTHVTSTLHICWGAQAGLYHHYGIPKHELPAKLFGVFEHFVYDPTEPLV 180

Query: 181 QGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSC 240
           +GFD+LF+APHSR+TEVR+ DI +V  L LLA+SEEAG ++++ ++  QVF  GH EY  
Sbjct: 181 RGFDDLFWAPHSRYTEVRKEDIEKVDNLILLADSEEAGPYIILSKDRSQVFITGHPEYDK 240

Query: 241 DTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQETPY 299
            TL +EY+RD+ KGL+  +PKNY+ +D+P+++ +VRWRSH  LL+SNWLNYYVYQ TPY
Sbjct: 241 LTLGEEYQRDQKKGLSTAIPKNYYLNDDPSKEAVVRWRSHAQLLYSNWLNYYVYQSTPY 299


Lambda     K      H
   0.319    0.136    0.403 

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: 319
Number of extensions: 7
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: 301
Length of database: 302
Length adjustment: 27
Effective length of query: 274
Effective length of database: 275
Effective search space:    75350
Effective search space used:    75350
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_010526168.1 GQW_RS0100790 (homoserine O-succinyltransferase)
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.1851086.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-144  465.9   0.5   3.8e-144  465.8   0.5    1.0  1  NCBI__GCF_000220155.1:WP_010526168.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010526168.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8   0.5  3.8e-144  3.8e-144       1     299 [.       1     300 [.       1     302 [] 1.00

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 3.8e-144
                             TIGR01001   1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllrid 73 
                                           mp+++pd lpa  ll+ en+fvm+e+ra +qdirpl++lilnlmp ki+te+ llr+lsn+plqv+++ll + 
  NCBI__GCF_000220155.1:WP_010526168.1   1 MPVNIPDLLPAKSLLEAENVFVMGESRAVTQDIRPLRILILNLMPLKIKTETHLLRVLSNTPLQVEVELLITS 73 
                                           9************************************************************************ PP

                             TIGR01001  74 srkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaq 146
                                           ++++kntp +hl  fyk+++e+k +++dG+i+tGapvell+fe+v yw+el++i++wsk++vtstl+icw+aq
  NCBI__GCF_000220155.1:WP_010526168.1  74 THTPKNTPSQHLISFYKTFDEIKGKNYDGFIITGAPVELLDFEKVTYWNELQKIMDWSKTHVTSTLHICWGAQ 146
                                           ************************************************************************* PP

                             TIGR01001 147 aalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagv 218
                                           a+l+  ygipk++l+ kl+Gv++h +  ++++l+rgfdd f+aphsry+++ +e+i+++ +l +la+s+eag 
  NCBI__GCF_000220155.1:WP_010526168.1 147 AGLYHHYGIPKHELPAKLFGVFEHFVYdPTEPLVRGFDDLFWAPHSRYTEVRKEDIEKVDNLILLADSEEAGP 219
                                           **************************9999******************************************* PP

                             TIGR01001 219 ylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnya 291
                                           y+++skd+ ++f+tGhpeydk tl +ey rd ++gl+ +ipknyy +ddp+k+ ++ wrsha+ll++nwlny+
  NCBI__GCF_000220155.1:WP_010526168.1 220 YIILSKDRSQVFITGHPEYDKLTLGEEYQRDQKKGLSTAIPKNYYLNDDPSKEAVVRWRSHAQLLYSNWLNYY 292
                                           ************************************************************************* PP

                             TIGR01001 292 vyqktpyd 299
                                           vyq+tpyd
  NCBI__GCF_000220155.1:WP_010526168.1 293 VYQSTPYD 300
                                           *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (301 nodes)
Target sequences:                          1  (302 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: 19.67
//
[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