Alignments for a candidate for metX in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Sulfuricurvum kujiense DSM 16994

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_013459654.1 SULKU_RS04030 homoserine O-acetyltransferase

Query= SwissProt::E0UR96
         (368 letters)



>NCBI__GCF_000183725.1:WP_013459654.1
          Length = 365

 Score =  590 bits (1522), Expect = e-173
 Identities = 270/364 (74%), Positives = 320/364 (87%)

Query: 3   LNLQTYTEHFTNPLYLESGRILEPYDITYETYGTMNEDKSNVVVVCHALTGSHHAAGLYE 62
           LNLQ ++EHFTNPLYLESGRILEPYDI YETYG +NE + NV+V+CHALTGSHHAAG YE
Sbjct: 2   LNLQIHSEHFTNPLYLESGRILEPYDIVYETYGELNEARDNVIVICHALTGSHHAAGTYE 61

Query: 63  DETKPGWWDGFIGSGKAIDTDKYFVICSNVIGSCFGSTGPMSLQHPYQEPYRYKFPVVSI 122
            + KPGWWDG IG GKA+DTD++FVIC+NVIGSCFGSTGPMSL++PY +PYRYKFPV++I
Sbjct: 62  GDNKPGWWDGLIGQGKAVDTDRFFVICTNVIGSCFGSTGPMSLRYPYNDPYRYKFPVITI 121

Query: 123 KDMVKAQRILFDRLDIHRVHAIVGGSMGGMQALQFAIHYPNFANKIIALATTHATQPWAI 182
            DMVKAQRILFDRL IH+VHA++GGSMGGMQAL F + +PNFA KIIA+ATT ATQPWAI
Sbjct: 122 LDMVKAQRILFDRLGIHQVHAVIGGSMGGMQALAFGVFFPNFAKKIIAMATTAATQPWAI 181

Query: 183 AFNKVAQESILNDPDFKQGYYDPDLLKEQGLSGMAVGRMAGHISFLSHESMREKFGRDYK 242
           AFNKVAQE+IL DP+FK GYYDP++++E GLSGMA+GRMAGHISFLSH+SM +KFGR+YK
Sbjct: 182 AFNKVAQEAILKDPEFKNGYYDPEVIRENGLSGMAIGRMAGHISFLSHQSMAKKFGREYK 241

Query: 243 LTDGLYELFGKFQVESYLEYNGYNFTKWFDPLAYLYITKAINIYDLSRGFDSLAEALKRV 302
            TDGL+ELFGKFQVESYLEYNGYNFTKWFDPL+YLYITKAINIYDLSRGFDS+ EAL ++
Sbjct: 242 RTDGLFELFGKFQVESYLEYNGYNFTKWFDPLSYLYITKAINIYDLSRGFDSIEEALNKI 301

Query: 303 TSALYLVSFKNDLLFKNFEMKEIADELDKIGNKNHSYIDVKSDYGHDAFLVELNKFENHV 362
            + LYLV F+ D+LF   EM+ I   +  +G  N  Y++V SDYGHDAFLVE++K EN+V
Sbjct: 302 NAELYLVGFEKDILFLPSEMESIHTAMLAMGKTNSDYLEVVSDYGHDAFLVEIDKIENYV 361

Query: 363 KDAL 366
           ++AL
Sbjct: 362 REAL 365


Lambda     K      H
   0.320    0.138    0.417 

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: 604
Number of extensions: 29
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: 368
Length of database: 365
Length adjustment: 30
Effective length of query: 338
Effective length of database: 335
Effective search space:   113230
Effective search space used:   113230
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_013459654.1 SULKU_RS04030 (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.25940.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-128  413.2   0.0   4.9e-128  413.0   0.0    1.0  1  lcl|NCBI__GCF_000183725.1:WP_013459654.1  SULKU_RS04030 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013459654.1  SULKU_RS04030 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.0   0.0  4.9e-128  4.9e-128       3     349 ..      13     364 ..      11     365 .] 0.96

  Alignments for each domain:
  == domain 1  score: 413.0 bits;  conditional E-value: 4.9e-128
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               ++l+lesG +l+ ++++y+tyG+ln++rdN++++cHaltgs+h+ag+++ ++k GWWd l+G+g+a+dt
  lcl|NCBI__GCF_000183725.1:WP_013459654.1  13 NPLYLESGRILEPYDIVYETYGELNEARDNVIVICHALTGSHHAAGTYEGDNKpGWWDGLIGQGKAVDT 81 
                                               789*********************************************998888*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +r+fv+c+Nv+Gsc GstgP+s+    ++py+ +fP++ti D+vkaq+ l d+Lg+++++av+GgS+GG
  lcl|NCBI__GCF_000183725.1:WP_013459654.1  82 DRFFVICTNVIGSCFGSTGPMSLRYPYNDPYRYKFPVITILDMVKAQRILFDRLGIHQVHAVIGGSMGG 150
                                               ************************999****************************************** PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee...qPekGLalAR 205
                                               mqal + ++ p+++kki+++at+a+++++aiafn+v+++ail+Dpe+++G+y+ e    +  +G+a+ R
  lcl|NCBI__GCF_000183725.1:WP_013459654.1 151 MQALAFGVFFPNFAKKIIAMATTAATQPWAIAFNKVAQEAILKDPEFKNGYYDPEVireNGLSGMAIGR 219
                                               ****************************************************99864336678999*** PP

                                 TIGR01392 206 mlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                               m ++++++s++s++++fgre k+++   ++l  +f+vesyl+y+g +f + Fd  sYl++tka++ +dl
  lcl|NCBI__GCF_000183725.1:WP_013459654.1 220 MAGHISFLSHQSMAKKFGREYKRTDG-LFELFGKFQVESYLEYNGYNFTKWFDPLSYLYITKAINIYDL 287
                                               *********************99966.667899************************************ PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle...yaeieseeGHDaFlleke 340
                                               +rg  ds++eal+ki+a+  +vg+e D+lf ++e e++++a+ a++++   y e+ s++GHDaFl+e +
  lcl|NCBI__GCF_000183725.1:WP_013459654.1 288 SRG-FDSIEEALNKINAELYLVGFEKDILFLPSEMESIHTAMLAMGKTnsdYLEVVSDYGHDAFLVEID 355
                                               ***.8**********************************999988877788****************** PP

                                 TIGR01392 341 kveeliref 349
                                               k+e+ +re 
  lcl|NCBI__GCF_000183725.1:WP_013459654.1 356 KIENYVREA 364
                                               *****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (365 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: 7.60
//
[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