Alignments for a candidate for metX in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Geobacter lovleyi SZ

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012471501.1 GLOV_RS17225 homoserine O-acetyltransferase

Query= SwissProt::B3E278
         (367 letters)



>NCBI__GCF_000020385.1:WP_012471501.1
          Length = 367

 Score =  762 bits (1968), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MSIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAG 60
           MSIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAG
Sbjct: 1   MSIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAG 60

Query: 61  KRREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFP 120
           KRREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFP
Sbjct: 61  KRREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFP 120

Query: 121 VITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPS 180
           VITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPS
Sbjct: 121 VITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPS 180

Query: 181 PQAISLNAVARWAIYNDPTWKKGEYKHNPKDGLALARGIGHITFLSDESMWQKFERRFSA 240
           PQAISLNAVARWAIYNDPTWKKGEYKHNPKDGLALARGIGHITFLSDESMWQKFERRFSA
Sbjct: 181 PQAISLNAVARWAIYNDPTWKKGEYKHNPKDGLALARGIGHITFLSDESMWQKFERRFSA 240

Query: 241 KDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRIT 300
           KDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRIT
Sbjct: 241 KDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRIT 300

Query: 301 APIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVRS 360
           APIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVRS
Sbjct: 301 APIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVRS 360

Query: 361 LLERVAP 367
           LLERVAP
Sbjct: 361 LLERVAP 367


Lambda     K      H
   0.323    0.138    0.439 

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: 624
Number of extensions: 13
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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: 49 (23.5 bits)

Align candidate WP_012471501.1 GLOV_RS17225 (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.2951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-134  433.6   0.0   3.1e-134  433.4   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012471501.1  GLOV_RS17225 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012471501.1  GLOV_RS17225 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.4   0.0  3.1e-134  3.1e-134       4     350 ..      16     362 ..      13     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 433.4 bits;  conditional E-value: 3.1e-134
                                 TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldt 70 
                                                + lesG +l  ++++y+ yGt+na+ +N+++v Ha tg+ah+agk  e+d+  GWWd ++Gpgr ldt
  lcl|NCBI__GCF_000020385.1:WP_012471501.1  16 GIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAGKRREDDPkpGWWDAIVGPGRLLDT 84 
                                               6789****************************************9988777678*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +ry+v+c+Nv+Gsc+GstgP+sinp+tgk+y  +fP++t+rD+v+aq+ lld+Lg+++l +v+GgS+GG
  lcl|NCBI__GCF_000020385.1:WP_012471501.1  85 DRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFPVITVRDMVRAQELLLDHLGIRRLLCVMGGSMGG 153
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmla 208
                                               mqalewa++yperv ++v+lat++r s+qai++n+v+r ai++Dp +++Gey++  +P+ GLalAR ++
  lcl|NCBI__GCF_000020385.1:WP_012471501.1 154 MQALEWATQYPERVASVVALATTPRPSPQAISLNAVARWAIYNDPTWKKGEYKH--NPKDGLALARGIG 220
                                               ****************************************************99..9************ PP

                                 TIGR01392 209 lltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlarg 277
                                               ++t++s+es+ ++f+r+ ++++   + +  +f+ve yl+y+g +fv+rFdAn++l+l+kald +d+a g
  lcl|NCBI__GCF_000020385.1:WP_012471501.1 221 HITFLSDESMWQKFERRFSAKDG-LFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWG 288
                                               ***************99999965.677999*************************************** PP

                                 TIGR01392 278 rrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekvee 344
                                                 +s+++a+++i+ap+ + +++sD+l+++ ++ee+++ l+  ++e  y+ i+s++GHDaFlle+e+++ 
  lcl|NCBI__GCF_000020385.1:WP_012471501.1 289 -YESMTDAFSRITAPIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEveYHLIQSAYGHDAFLLEHETFTP 356
                                               .8***************************************999889********************** PP

                                 TIGR01392 345 lirefl 350
                                               ++r++l
  lcl|NCBI__GCF_000020385.1:WP_012471501.1 357 MVRSLL 362
                                               **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (367 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.16
//
[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