Alignments for a candidate for metX in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Desulfotalea psychrophila LSv54

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_041277703.1 DP_RS06275 homoserine O-acetyltransferase

Query= SwissProt::C4XNQ9
         (397 letters)



>NCBI__GCF_000025945.1:WP_041277703.1
          Length = 390

 Score =  461 bits (1187), Expect = e-134
 Identities = 217/372 (58%), Positives = 283/372 (76%), Gaps = 3/372 (0%)

Query: 13  SVGRVEKRFFTVAEADSPLTVESGRALGPVVLAYETCGQLNERADNAVLVLHALTGDSHA 72
           SVG VEK+FFT A+  SPL +E+G  LGP+ +AYET G L+ R DNA+L+ HA +GDSH 
Sbjct: 10  SVGIVEKQFFTCAQVPSPLILENGAKLGPITIAYETYGNLSARKDNAILINHAFSGDSHV 69

Query: 73  AGYY--EPGDAKPGWWDLMIGPGKPIDTDRYYVICSNVIGGCMGSTGPSSLDPATGQPYG 130
           AG+Y  +    KPGWWD ++GPGK IDTD+Y++ICSN++G C G+TGP+S +  TG+ Y 
Sbjct: 70  AGHYATDGPKEKPGWWDFLVGPGKGIDTDKYFIICSNILGSCNGTTGPASKNSETGEAYA 129

Query: 131 LTFPVITIGDMVRAQKRLVEHLGVTKLLSVVGGSMGGMQALEWSVRYPDMVRTAVPLATT 190
           L FP++TIGDMV  QK L++HLG+ KLL+V+GGS+GGMQ LEW++RYP+M+ + +P+ATT
Sbjct: 130 LDFPMVTIGDMVATQKLLIDHLGIPKLLAVIGGSVGGMQTLEWAIRYPEMMHSVIPIATT 189

Query: 191 TKHSALAIAFNEVARQAIMADPNWNGGNYYDGVPPAHGLAVGRMIGHITYLSDEAMRQKF 250
            +HSALAIAFNE+ARQAIM DP+WN G YY    P  GLAV RM+GH+TYLSDEAMR+KF
Sbjct: 190 MRHSALAIAFNEIARQAIMTDPHWNRGKYYGQAHPDTGLAVARMVGHVTYLSDEAMRRKF 249

Query: 251 DRRLQDRCENSFVLEEPDFQVESYLRYQGQKFVDRFDANSFLYITKAADYFNLEASHGCG 310
            R LQ++ EN     + DFQVESYLRYQG KFV RFDANS LYITKA+DYF++       
Sbjct: 250 GRNLQEK-ENLSYGFDADFQVESYLRYQGNKFVHRFDANSLLYITKASDYFDIVERISTS 308

Query: 311 SAVAAFAKAKCRYLVASFSSDWLYPTYQSRSMVQAMKKNGLDVSFVELEAKWGHDAFLLP 370
                    + +YLV S+SSDWLYPTYQ+R +V+A+K++G +VSF E+E+  GHDAFL+P
Sbjct: 309 GPETELTAPQQKYLVISYSSDWLYPTYQARDLVKALKRSGRNVSFSEIESDCGHDAFLIP 368

Query: 371 NARLSGMIARFL 382
           + RL  ++  FL
Sbjct: 369 DDRLEQLMRGFL 380


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: 482
Number of extensions: 26
Number of successful extensions: 4
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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_041277703.1 DP_RS06275 (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.6270.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-141  456.6   0.0   3.3e-141  456.3   0.0    1.0  1  lcl|NCBI__GCF_000025945.1:WP_041277703.1  DP_RS06275 homoserine O-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_041277703.1  DP_RS06275 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.3   0.0  3.3e-141  3.3e-141       3     350 ..      26     380 ..      24     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 456.3 bits;  conditional E-value: 3.3e-141
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk....GWWdellGpgra 67 
                                               ++l le+G++l  +++ay+tyG+l+a++dNa+l+ Ha++g++hvag++ ++ +    GWWd l+Gpg+ 
  lcl|NCBI__GCF_000025945.1:WP_041277703.1  26 SPLILENGAKLGPITIAYETYGNLSARKDNAILINHAFSGDSHVAGHYATDGPkekpGWWDFLVGPGKG 94 
                                               5799******************************************99877656788************ PP

                                 TIGR01392  68 ldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgS 136
                                               +dt++yf++c+N lGsc+G+tgP+s n etg+ y  +fP+vti D+v +qk l+d+Lg+ kl av+GgS
  lcl|NCBI__GCF_000025945.1:WP_041277703.1  95 IDTDKYFIICSNILGSCNGTTGPASKNSETGEAYALDFPMVTIGDMVATQKLLIDHLGIPKLLAVIGGS 163
                                               ********************************************************************* PP

                                 TIGR01392 137 lGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalAR 205
                                               +GGmq+lewa++ype++++++++at++r+sa aiafne++rqai++Dp++n G+y+ + +P++GLa+AR
  lcl|NCBI__GCF_000025945.1:WP_041277703.1 164 VGGMQTLEWAIRYPEMMHSVIPIATTMRHSALAIAFNEIARQAIMTDPHWNRGKYYGQAHPDTGLAVAR 232
                                               ********************************************************************* PP

                                 TIGR01392 206 mlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                               m++++tY+s+e+++++fgr+ +++e+l++ ++++f+vesylryqg+kfv+rFdAns l++tka d++d+
  lcl|NCBI__GCF_000025945.1:WP_041277703.1 233 MVGHVTYLSDEAMRRKFGRNLQEKENLSYGFDADFQVESYLRYQGNKFVHRFDANSLLYITKASDYFDI 301
                                               ********************************************************************9 PP

                                 TIGR01392 275 argr.rdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFlleke 340
                                                +   + + +  l++ ++++lv++++sD+l+++ ++++l+kalk+++ +  + eies+ GHDaFl+ ++
  lcl|NCBI__GCF_000025945.1:WP_041277703.1 302 VERIsTSGPETELTAPQQKYLVISYSSDWLYPTYQARDLVKALKRSGRNvsFSEIESDCGHDAFLIPDD 370
                                               987646678889*********************************999889****************** PP

                                 TIGR01392 341 kveelirefl 350
                                               ++e+l+r fl
  lcl|NCBI__GCF_000025945.1:WP_041277703.1 371 RLEQLMRGFL 380
                                               ******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (390 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.47
//
[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