Alignments for a candidate for metX in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Echinicola vietnamensis KMM 6221, DSM 17526

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Echvi_3285 Echvi_3285 homoserine O-acetyltransferase

Query= SwissProt::G0J5N4
         (351 letters)



>FitnessBrowser__Cola:Echvi_3285
          Length = 351

 Score =  556 bits (1433), Expect = e-163
 Identities = 260/350 (74%), Positives = 304/350 (86%)

Query: 1   MNLQSPHLTIEMTQEIFYCQEALSLESGESFPEFQLSFTTQGQLNANKDNVIWVLHALTG 60
           MNL SP+L  +MTQE F+C+E L+LESGES P F++S+TTQG L   KDNVIW+LHALTG
Sbjct: 1   MNLTSPYLITDMTQETFHCEEELNLESGESLPGFEISYTTQGHLTPKKDNVIWILHALTG 60

Query: 61  DANPHEWWSGLIGEDKFFDPSKYFIVCANFLGSCYGSTQPLSNNPNNGKPYYYDFPNITT 120
           DAN HEWWSGL+GEDKFFDP+KYFIVCAN LGSCYGSTQPLS+NP  GKPYYYDFPN++T
Sbjct: 61  DANVHEWWSGLVGEDKFFDPTKYFIVCANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLST 120

Query: 121 RDIASALDKLRIHLGLEKINTVIGGSLGGQVGLEWAVSLGEKLENAIIVASNAKASPWII 180
           RD+A A D+LR HLG+++I+T+IGGSLGGQV LEW+ +L E+++  IIVASNAK SPW I
Sbjct: 121 RDMAKAFDRLRQHLGIQQIDTIIGGSLGGQVALEWSYNLQEQVKKTIIVASNAKTSPWTI 180

Query: 181 GFNETQRMAIESDSTWGKTQPEAGKKGLETARAIGMLSYRHPMTFLQNQSETEEKRDDFK 240
           GFNE QRMAIESDSTWG+  P+AGKKGLE ARAIGMLSYRH   F  +Q+ETEEK D F+
Sbjct: 181 GFNEAQRMAIESDSTWGQNSPDAGKKGLEAARAIGMLSYRHQDIFHASQAETEEKTDHFR 240

Query: 241 ISSYLRYQGLKLANRFNAMSYWILSKAMDSHDIGRGRGGTPVALSNIKCKVLSIGVDTDI 300
           +SSYLRYQG KL+NRFNA+SYW+L+KAMDSHD+GRGRGGT  ALS IK KVLSIG++TD+
Sbjct: 241 VSSYLRYQGQKLSNRFNALSYWVLTKAMDSHDLGRGRGGTAKALSAIKAKVLSIGINTDL 300

Query: 301 LFTSEESRYISKHVPKGTYREISSIYGHDAFLIEYEQLQYILKSFYLENN 350
           LFT EES++ISK+VP GTYREISSIYGHDAFL+E EQL YIL SFYLENN
Sbjct: 301 LFTKEESQFISKNVPNGTYREISSIYGHDAFLVENEQLNYILTSFYLENN 350


Lambda     K      H
   0.317    0.134    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: 478
Number of extensions: 6
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: 351
Length of database: 351
Length adjustment: 29
Effective length of query: 322
Effective length of database: 322
Effective search space:   103684
Effective search space used:   103684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_3285 Echvi_3285 (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.2359.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     2e-111  358.4   0.1   2.3e-111  358.2   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3285  Echvi_3285 homoserine O-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3285  Echvi_3285 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.2   0.1  2.3e-111  2.3e-111       3     349 ..      21     345 ..      19     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 2.3e-111
                            TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldtsryfvv 76 
                                          eel+lesGe l+ +e+ y t G+l+ ++dN++ ++Haltg+a+v+   +     WW+ l+G+++ +d+++yf+v
  lcl|FitnessBrowser__Cola:Echvi_3285  21 EELNLESGESLPGFEISYTTQGHLTPKKDNVIWILHALTGDANVH---E-----WWSGLVGEDKFFDPTKYFIV 86 
                                          79******************************************9...6.....******************** PP

                            TIGR01392  77 clNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsyp 150
                                          c+N lGsc+Gst Pls np+tgkpy  +fP++++rD++ka  +l ++Lg++++ +++GgSlGG  alew+ + +
  lcl|FitnessBrowser__Cola:Echvi_3285  87 CANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLSTRDMAKAFDRLRQHLGIQQIDTIIGGSLGGQVALEWSYNLQ 160
                                          ************************************************************************** PP

                            TIGR01392 151 ervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesleerfgr 224
                                          e+vkk++ +a+ a++s+++i+fne+qr+ai+sD  + + + +     +kGL++AR +++l+Yr ++ +++  ++
  lcl|FitnessBrowser__Cola:Echvi_3285 161 EQVKKTIIVASNAKTSPWTIGFNEAQRMAIESDSTWGQNSPDA---GKKGLEAARAIGMLSYRHQDIFHASQAE 231
                                          ************************************7766665...78***************99988766553 PP

                            TIGR01392 225 eakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgi 298
                                          ++++        +++f v+sylryqg+k+ +rF+A sY +ltka+d+hdl+rg r+++++al++ika+vl +gi
  lcl|FitnessBrowser__Cola:Echvi_3285 232 TEEK--------TDHFRVSSYLRYQGQKLSNRFNALSYWVLTKAMDSHDLGRG-RGGTAKALSAIKAKVLSIGI 296
                                          3333........468**************************************.89****************** PP

                            TIGR01392 299 esDllftleeqeelakalkaakleyaeieseeGHDaFllekekveeliref 349
                                          ++Dllft ee++ ++k++++ + +  ei+s +GHDaFl+e+e+++ ++++f
  lcl|FitnessBrowser__Cola:Echvi_3285 297 NTDLLFTKEESQFISKNVPNGTYR--EISSIYGHDAFLVENEQLNYILTSF 345
                                          *******************99866..*******************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (351 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: 00:00:00.02
# Mc/sec: 6.08
//
[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