Alignments for a candidate for metX in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Kyrpidia tusciae DSM 2912

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_013074689.1 BTUS_RS03205 homoserine O-acetyltransferase

Query= SwissProt::C4XNQ9
         (397 letters)



>NCBI__GCF_000092905.1:WP_013074689.1
          Length = 373

 Score =  350 bits (899), Expect = e-101
 Identities = 178/357 (49%), Positives = 237/357 (66%), Gaps = 8/357 (2%)

Query: 30  PLTVESGRALGPVVLAYETCGQLNERADNAVLVLHALTGDSHAAGYYEPGDAKPGWWDLM 89
           PLT+ESGR L  V +AYE  G      D  +LV HALTGD+HA       D +PGWWD +
Sbjct: 15  PLTLESGRVLDEVDIAYEAYGDPENARDRTILVCHALTGDAHAGNL----DGQPGWWDGL 70

Query: 90  IGPGKPIDTDRYYVICSNVIGGCMGSTGPSSLDPATGQPYGLTFPVITIGDMVRAQKRLV 149
           IGPG+ +DTDR+Y++CSNV+GGC GSTGP+S  P  G+P+GL FP ITI DMV AQ+  +
Sbjct: 71  IGPGRVLDTDRFYIVCSNVLGGCAGSTGPASPGP-DGRPWGLRFPPITIRDMVEAQRLWL 129

Query: 150 EHLGVTKLLSVVGGSMGGMQALEWSVRYPDMVRTAVPLATTTKHSALAIAFNEVARQAIM 209
           E LG+T L +V+GGSMGGMQALEW+V YPD V   +P+AT+ + SA+AIA+N+V R AIM
Sbjct: 130 EKLGITHLYAVIGGSMGGMQALEWAVTYPDRVERCIPIATSARLSAMAIAYNDVMRLAIM 189

Query: 210 ADPNWNGGNYYDGVPPAHGLAVGRMIGHITYLSDEAMRQKFDRRLQDRCENSFVLE-EPD 268
            DP WNGG+YY+G  PA GLA+ RM+G ITY   +    +F R +  R E    ++ E  
Sbjct: 190 NDPMWNGGDYYNGEKPAAGLALARMVGMITYRGPQLYNARFGRSVVGREEADGPVDFEAR 249

Query: 269 FQVESYLRYQGQKFVDRFDANSFLYITKAADYFNLEASHGCGSAVAAFAKAKCRYLVASF 328
           FQVESYLRYQG+K V RFDANS+LY+ KA D  ++    G G   AA+A+ +  +L    
Sbjct: 250 FQVESYLRYQGEKLVRRFDANSYLYLIKAMDLHDI--GRGRGGVHAAYARTEAEFLCIGI 307

Query: 329 SSDWLYPTYQSRSMVQAMKKNGLDVSFVELEAKWGHDAFLLPNARLSGMIARFLDRA 385
            SD LYP  +   + + +   G  V + E+ + +GHDAFL+   ++SG +  FL+ A
Sbjct: 308 DSDILYPAAEQIEIAEGLAATGKRVQYREIRSVYGHDAFLVEFQQMSGALGEFLNPA 364


Lambda     K      H
   0.320    0.135    0.411 

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: 463
Number of extensions: 23
Number of successful extensions: 5
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: 397
Length of database: 373
Length adjustment: 30
Effective length of query: 367
Effective length of database: 343
Effective search space:   125881
Effective search space used:   125881
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: 50 (23.9 bits)

Align candidate WP_013074689.1 BTUS_RS03205 (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.3644.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-143  464.5   0.0   1.3e-143  464.3   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074689.1  BTUS_RS03205 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074689.1  BTUS_RS03205 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.3   0.0  1.3e-143  1.3e-143       3     350 ..      14     361 ..      12     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.3 bits;  conditional E-value: 1.3e-143
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldts 71 
                                                +ltlesG vl+ev++ay+ yG+ +++rd ++lvcHaltg+ah+ +  d +++GWWd l+Gpgr ldt+
  lcl|NCBI__GCF_000092905.1:WP_013074689.1  14 GPLTLESGRVLDEVDIAYEAYGDPENARDRTILVCHALTGDAHAGN-LD-GQPGWWDGLIGPGRVLDTD 80 
                                               689*****************************************94.44.799**************** PP

                                 TIGR01392  72 ryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGm 140
                                               r+++vc+NvlG+c GstgP+s  p+ g+p+g +fP +tirD+v+aq+  l++Lg+++l av+GgS+GGm
  lcl|NCBI__GCF_000092905.1:WP_013074689.1  81 RFYIVCSNVLGGCAGSTGPASPGPD-GRPWGLRFPPITIRDMVEAQRLWLEKLGITHLYAVIGGSMGGM 148
                                               ************************9.******************************************* PP

                                 TIGR01392 141 qalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlal 209
                                               qalewa++yp+rv++++++atsar+sa+aia+n+v+r ai++Dp +n+G+y++ e+P++GLalARm+++
  lcl|NCBI__GCF_000092905.1:WP_013074689.1 149 QALEWAVTYPDRVERCIPIATSARLSAMAIAYNDVMRLAIMNDPMWNGGDYYNGEKPAAGLALARMVGM 217
                                               ********************************************************************* PP

                                 TIGR01392 210 ltYrseesleerfgreakseeslassl..eeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276
                                               +tYr+ + +++rfgr++  +e+ +  +  e++f+vesylryqg+k+v+rFdAnsYl+l ka+d hd++r
  lcl|NCBI__GCF_000092905.1:WP_013074689.1 218 ITYRGPQLYNARFGRSVVGREEADGPVdfEARFQVESYLRYQGEKLVRRFDANSYLYLIKAMDLHDIGR 286
                                               ****************9999877765444**************************************** PP

                                 TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343
                                               g r+++++a ++++a++l +gi+sD+l++++eq e+a+ l a++++  y+ei+s +GHDaFl+e+++++
  lcl|NCBI__GCF_000092905.1:WP_013074689.1 287 G-RGGVHAAYARTEAEFLCIGIDSDILYPAAEQIEIAEGLAATGKRvqYREIRSVYGHDAFLVEFQQMS 354
                                               *.8**************************************9999889********************* PP

                                 TIGR01392 344 elirefl 350
                                                ++ efl
  lcl|NCBI__GCF_000092905.1:WP_013074689.1 355 GALGEFL 361
                                               9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (373 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: 00:00:00.01
# Mc/sec: 10.81
//
[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