Alignments for a candidate for metX in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Chlorobaculum parvum NCIB 8327

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012501875.1 CPAR_RS03180 homoserine O-acetyltransferase

Query= SwissProt::Q3M5Q6
         (359 letters)



>NCBI__GCF_000020505.1:WP_012501875.1
          Length = 356

 Score =  390 bits (1002), Expect = e-113
 Identities = 191/350 (54%), Positives = 244/350 (69%), Gaps = 2/350 (0%)

Query: 1   MNYQDFISEQTEYYHLPVPFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSAD 60
           M Y   IS+ T  +    PF LE GG L  +++AYRTWG LN+   N +L+CHALTG+AD
Sbjct: 4   MEYIPIISDSTSSFKSYDPFPLELGGELPELKIAYRTWGTLNAQKSNVILVCHALTGNAD 63

Query: 61  ADEWWEGLLGANKALDSDRDFIICSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDM 120
           AD WW G+ G  KA D  +DFIICSN++GSCYG+TG  S+NP++G  YG  FP ITIRDM
Sbjct: 64  ADSWWRGMFGEGKAFDETKDFIICSNVIGSCYGSTGPLSLNPKSGKRYGPDFPRITIRDM 123

Query: 121 VRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLS 180
           V  Q  L+Q  GI+ ++LVIG SLGGMQVLEW  +YPE+  A+ P+  SGRHSAWCI  S
Sbjct: 124 VAAQRLLLQSFGIEKIKLVIGASLGGMQVLEWGAMYPEMAGALMPMGISGRHSAWCIAQS 183

Query: 181 EAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARFGRQYDAVADQF 240
           EAQRQAI AD  W+GG Y   Q P +GLA ARMMAM  YR ++++  RFGR+       F
Sbjct: 184 EAQRQAIAADAEWQGGWYDPAQQPRKGLAAARMMAMCTYRCFENYEERFGRE-QREDGLF 242

Query: 241 AIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQGRD-YKSVLQSIKQPALVVAIDSD 299
              SY++H G KLV RFDANTYITLT+AMD HD+ +GR+ Y++ L +   P  +++IDSD
Sbjct: 243 EAESYMRHQGDKLVGRFDANTYITLTRAMDMHDLGRGRESYEAALGAFTMPVEILSIDSD 302

Query: 300 ILYPPTEQQELADFIPDAQLGWLQSSYGHDAFLIDIATLSQLVINFRQSL 349
           ILYP  EQ+ELA  IP ++L +L   YGHDAFLID  T+S++   F++ L
Sbjct: 303 ILYPKQEQEELARLIPGSRLLFLDEPYGHDAFLIDTDTVSRMACEFKRQL 352


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: 406
Number of extensions: 17
Number of successful extensions: 3
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: 356
Length adjustment: 29
Effective length of query: 330
Effective length of database: 327
Effective search space:   107910
Effective search space used:   107910
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_012501875.1 CPAR_RS03180 (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.641168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-140  453.7   0.0   2.4e-140  453.5   0.0    1.0  1  NCBI__GCF_000020505.1:WP_012501875.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020505.1:WP_012501875.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.5   0.0  2.4e-140  2.4e-140       3     349 ..      21     348 ..      19     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 453.5 bits;  conditional E-value: 2.4e-140
                             TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldtsryfv 75 
                                           +++ le+G++l+e+++ay+t+Gtlna+++N++lvcHaltg+a+++   +     WW+ ++G+g+a+d+++ f+
  NCBI__GCF_000020505.1:WP_012501875.1  21 DPFPLELGGELPELKIAYRTWGTLNAQKSNVILVCHALTGNADAD---S-----WWRGMFGEGKAFDETKDFI 85 
                                           6899***************************************99...5.....******************* PP

                             TIGR01392  76 vclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewals 148
                                           +c+Nv+Gsc+GstgPls+np++gk+yg++fP++tirD+v aq+ ll+s+g+ek+++v+G+SlGGmq+lew ++
  NCBI__GCF_000020505.1:WP_012501875.1  86 ICSNVIGSCYGSTGPLSLNPKSGKRYGPDFPRITIRDMVAAQRLLLQSFGIEKIKLVIGASLGGMQVLEWGAM 158
                                           ************************************************************************* PP

                             TIGR01392 149 ypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesleer 221
                                           ype++ +++++  s r+sa++ia +e+qrqai++D+e+++G+y+  +qP+kGLa+ARm+a++tYr+ e++eer
  NCBI__GCF_000020505.1:WP_012501875.1 159 YPEMAGALMPMGISGRHSAWCIAQSEAQRQAIAADAEWQGGWYDPAQQPRKGLAAARMMAMCTYRCFENYEER 231
                                           ************************************************************************* PP

                             TIGR01392 222 fgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvl 294
                                           fgre++++          f++esy+r+qg+k+v rFdAn+Y++lt+a+d+hdl+rg r+s+++al ++++pv 
  NCBI__GCF_000020505.1:WP_012501875.1 232 FGREQRED--------GLFEAESYMRHQGDKLVGRFDANTYITLTRAMDMHDLGRG-RESYEAALGAFTMPVE 295
                                           **887776........689*************************************.8*************** PP

                             TIGR01392 295 vvgiesDllftleeqeelakalkaakleyaeieseeGHDaFllekekveeliref 349
                                           +++i+sD+l++ +eqeela+ ++ ++l    +++++GHDaFl+++++v+++  ef
  NCBI__GCF_000020505.1:WP_012501875.1 296 ILSIDSDILYPKQEQEELARLIPGSRLL--FLDEPYGHDAFLIDTDTVSRMACEF 348
                                           ****************************..9******************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (356 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: 00:00:00.00
# Mc/sec: 20.20
//
[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