Alignments for a candidate for metX in Thiomicrospira pelophila DSM 1534

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Thiomicrospira pelophila DSM 1534

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_029933743.1 N746_RS0102275 homoserine O-acetyltransferase

Query= SwissProt::K2QXP6
         (493 letters)



>NCBI__GCF_000711195.1:WP_029933743.1
          Length = 379

 Score =  392 bits (1007), Expect = e-113
 Identities = 193/357 (54%), Positives = 258/357 (72%), Gaps = 6/357 (1%)

Query: 3   KESVGVVETKHYNLSEELILDGGDSLKDVTIAYETYGTLNKQKSNAILVCHALSGNAHVA 62
           K S+G V  +  ++ E L L  G  L    + YETYG+LN + +NAIL+CHALSG+ HVA
Sbjct: 2   KNSIGTVTPQTLHVDEPLALVSGAVLPQYDLVYETYGSLNAEANNAILICHALSGDHHVA 61

Query: 63  GWHEGDRKPGWWDNIIGPGKCLDTDRYFIICSNVLGGCQGSTGPSSLNPETGKQYALEFP 122
           G++EGD KPGWW++ IGPGK +DT+ +F++CSN LG C+GSTGP+SLNPETGK +  +FP
Sbjct: 62  GFYEGDDKPGWWNDYIGPGKPIDTNEFFVVCSNNLGSCRGSTGPTSLNPETGKVFGSDFP 121

Query: 123 IITIKDMVKAQKKLIDHLQIKQLFSVVGGSMGGMQVLQWCVSYPDMVRSAIPIATTSYSS 182
           I+T +D V +Q +L  HL I+Q  ++VGGSMGGMQV+QW + YPD +R A+ IA     S
Sbjct: 122 IVTCRDWVHSQNQLRQHLGIEQWAAIVGGSMGGMQVMQWAIDYPDKLRHAVVIAAAPKLS 181

Query: 183 PQQIAFNEVGRRAIISDPHWNEGNYYE-GEFPDSGLALARMIGHITYLSNESMYEKFGRR 241
            Q IAFNEV RRAI++DP ++EG + E G  P  GLALARM+GH+TYLS++ M  KFGR 
Sbjct: 182 AQNIAFNEVARRAIMTDPEFHEGRFIEAGTIPKGGLALARMLGHLTYLSDDMMGAKFGRE 241

Query: 242 LQ-DKEEYSFDFSTDFEVESYLHYQGDTFT--KRFDANSYLYISKAIDYFDLTENGTVSL 298
           L+ DK +YSF+   +F+VESYL YQG+ F   + FDAN+YL ++KA+DYFD        L
Sbjct: 242 LRADKLKYSFE--VEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPASEFDNDL 299

Query: 299 SEALKNVKARVLVISVDSDWLYTPAESKEIVMAMTANEVDVSYCQIKSSYGHDAFLL 355
           S+A  N KA+ LVIS  SDW ++PA S+EIV A+  N++ VSY ++ S +GHDAFLL
Sbjct: 300 SQAFANTKAQFLVISFTSDWRFSPARSREIVRALLDNDLSVSYAEVVSEHGHDAFLL 356


Lambda     K      H
   0.317    0.134    0.391 

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: 486
Number of extensions: 18
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: 493
Length of database: 379
Length adjustment: 32
Effective length of query: 461
Effective length of database: 347
Effective search space:   159967
Effective search space used:   159967
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_029933743.1 N746_RS0102275 (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.3879704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-143  462.1   0.0     7e-143  461.9   0.0    1.0  1  NCBI__GCF_000711195.1:WP_029933743.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711195.1:WP_029933743.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.9   0.0    7e-143    7e-143       3     349 ..      17     368 ..      15     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 461.9 bits;  conditional E-value: 7e-143
                             TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsryf 74 
                                           e+l l sG+vl++++++y+tyG lnae +Na+l+cHal+g++hvag ++ +dk GWW++++Gpg+++dt+++f
  NCBI__GCF_000711195.1:WP_029933743.1  17 EPLALVSGAVLPQYDLVYETYGSLNAEANNAILICHALSGDHHVAGFYEGDDKpGWWNDYIGPGKPIDTNEFF 89 
                                           7899*******************************************9988888******************* PP

                             TIGR01392  75 vvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewal 147
                                           vvc+N+lGsc+GstgP+s+npetgk +g++fP vt rD+v+ q++l ++Lg+e++aa+vGgS+GGmq+++wa+
  NCBI__GCF_000711195.1:WP_029933743.1  90 VVCSNNLGSCRGSTGPTSLNPETGKVFGSDFPIVTCRDWVHSQNQLRQHLGIEQWAAIVGGSMGGMQVMQWAI 162
                                           ************************************************************************* PP

                             TIGR01392 148 sypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesle 219
                                           +yp++++++vv+a+++++saq+iafnev+r+ai++Dpe+++G++ e +  P+ GLalARml++ltY+s++ + 
  NCBI__GCF_000711195.1:WP_029933743.1 163 DYPDKLRHAVVIAAAPKLSAQNIAFNEVARRAIMTDPEFHEGRFIEAGtIPKGGLALARMLGHLTYLSDDMMG 235
                                           **********************************************9999*********************** PP

                             TIGR01392 220 erfgreakseeslassleeefsvesylryqgkkfver..FdAnsYllltkaldthdlargrrdslkealkkik 290
                                           ++fgre +++ +l++s+e ef+vesylryqg+kf+++  FdAn+Yll+tkald++d a + +++l++a++++k
  NCBI__GCF_000711195.1:WP_029933743.1 236 AKFGRELRAD-KLKYSFEVEFQVESYLRYQGEKFATKqnFDANTYLLMTKALDYFDPASEFDNDLSQAFANTK 307
                                           *****99998.78899******************96444********************************** PP

                             TIGR01392 291 apvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveeliref 349
                                           a++lv++++sD++f++++++e+++al +++l+  yae+ se+GHDaFll ++++e + +++
  NCBI__GCF_000711195.1:WP_029933743.1 308 AQFLVISFTSDWRFSPARSREIVRALLDNDLSvsYAEVVSEHGHDAFLLPNTHYEGVFHAY 368
                                           **************************99999889***************999998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (379 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 16.02
//
[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