Alignments for a candidate for metX in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Thiomicrospira cyclica ALM1

Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_013834891.1 THICY_RS01725 homoserine O-acetyltransferase

Query= curated2:Q1QQD3
         (399 letters)



>NCBI__GCF_000214825.1:WP_013834891.1
          Length = 377

 Score =  380 bits (975), Expect = e-110
 Identities = 188/364 (51%), Positives = 251/364 (68%), Gaps = 8/364 (2%)

Query: 24  TSQVAMFAGDQPLPLDCGIDLAPFQIAYQTYGELNAGKSNAILVCHALTGDQHVANVHPV 83
           T QV+M     PL L  G +L  + + Y+TYGELNA  SNA+L+CHAL+GD HV   +  
Sbjct: 11  TLQVSM-----PLQLVSGAELPSYDLVYETYGELNADASNAVLICHALSGDHHVTGYYEG 65

Query: 84  TGKPGWWVTLVGPGKPLDTDKYFVICSNVIGGCMGSTGPASTNPATGTVWGLDFPVITIP 143
             KPGWW   +GPGKP+DT+++FV+CSN +GGC GS+GPAS NPATG V+G DFP++T  
Sbjct: 66  DTKPGWWSDYIGPGKPVDTNEFFVVCSNNLGGCRGSSGPASLNPATGKVYGPDFPIVTCR 125

Query: 144 DMVRAQAMLIDRLGIDTLFSVVGGSMGGMQVLQWCVAYPQRVFSALPIACSTRHSAQNIA 203
           D V +Q  L   LGI+   +V+GGSMGGMQV+QW + +P ++  AL IA + + SAQNIA
Sbjct: 126 DWVNSQNTLRQHLGIEQWAAVIGGSMGGMQVMQWAIDHPDKLRHALVIAAAPKLSAQNIA 185

Query: 204 FHELGRQAVMADPDWRDGRYVEQGTYPHRGLGVARMAAHITYLSDAALHRKFGRRMQDRD 263
           F+E+ R+A+M DP++  GR++E GT P  GL +ARM  H+TYLSD  +  KFGR ++   
Sbjct: 186 FNEVARRAIMTDPEFNGGRFIEAGTTPKGGLALARMLGHLTYLSDDMMGAKFGRELRSES 245

Query: 264 LPTFSFDADFQVESYLRHQGSSFV--ERFDANSYLYLTRAMDYFDIAADHNGVLAAAFRD 321
           L  +SFD +FQVESYLR+QG  F   + FDAN+YL +T+A+DYFD AA+ +  L+AAF  
Sbjct: 246 L-KYSFDVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPAAEFDNNLSAAFAQ 304

Query: 322 TRTRFCVVSFTSDWLFPTSESRATVHALNAGGARVSFAEIETDRGHDAFLLDLPEFFDIA 381
           T+  F VVSFTSDW F  + SR  V AL      VS+AEIE++ GHDAFLL    +  I 
Sbjct: 305 TQASFLVVSFTSDWRFSPTRSREIVRALLDNDRAVSYAEIESEHGHDAFLLPNTHYEGIF 364

Query: 382 HAFL 385
            A++
Sbjct: 365 RAYM 368


Lambda     K      H
   0.323    0.136    0.427 

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: 464
Number of extensions: 19
Number of successful extensions: 3
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: 399
Length of database: 377
Length adjustment: 30
Effective length of query: 369
Effective length of database: 347
Effective search space:   128043
Effective search space used:   128043
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_013834891.1 THICY_RS01725 (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.16397.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-142  461.1   0.0   1.4e-142  460.9   0.0    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013834891.1  THICY_RS01725 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013834891.1  THICY_RS01725 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.9   0.0  1.4e-142  1.4e-142       3     350 ..      16     368 ..      14     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 460.9 bits;  conditional E-value: 1.4e-142
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                                +l+l sG++l++++++y+tyG+lna+ +Navl+cHal+g++hv+g+++ ++k GWW++++Gpg+++dt
  lcl|NCBI__GCF_000214825.1:WP_013834891.1  16 MPLQLVSGAELPSYDLVYETYGELNADASNAVLICHALSGDHHVTGYYEGDTKpGWWSDYIGPGKPVDT 84 
                                               5899*********************************************99889*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +++fvvc+N+lG+c+Gs+gP+s+np+tgk yg++fP vt rD+v+ q++l ++Lg+e++aav+GgS+GG
  lcl|NCBI__GCF_000214825.1:WP_013834891.1  85 NEFFVVCSNNLGGCRGSSGPASLNPATGKVYGPDFPIVTCRDWVNSQNTLRQHLGIEQWAAVIGGSMGG 153
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+++wa++ p+++++++v+a+++++saq+iafnev+r+ai++Dpe+n+G++ e + +P+ GLalARml
  lcl|NCBI__GCF_000214825.1:WP_013834891.1 154 MQVMQWAIDHPDKLRHALVIAAAPKLSAQNIAFNEVARRAIMTDPEFNGGRFIEAGtTPKGGLALARML 222
                                               ******************************************************999************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfver..FdAnsYllltkaldthdl 274
                                               ++ltY+s++ + ++fgre +se sl++s++ ef+vesylryqg+kf+++  FdAn+Yll+tkald++d 
  lcl|NCBI__GCF_000214825.1:WP_013834891.1 223 GHLTYLSDDMMGAKFGRELRSE-SLKYSFDVEFQVESYLRYQGEKFATKqnFDANTYLLMTKALDYFDP 290
                                               ******************9998.88999******************96444****************** PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                               a++ +++l++a+++++a++lvv+++sD++f++++++e+++al +++ +  yaeiese+GHDaFll +++
  lcl|NCBI__GCF_000214825.1:WP_013834891.1 291 AAEFDNNLSAAFAQTQASFLVVSFTSDWRFSPTRSREIVRALLDNDRAvsYAEIESEHGHDAFLLPNTH 359
                                               *****************************************999887778******************9 PP

                                 TIGR01392 342 veelirefl 350
                                               +e + r+++
  lcl|NCBI__GCF_000214825.1:WP_013834891.1 360 YEGIFRAYM 368
                                               999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (377 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: 00:00:00.01
# Mc/sec: 10.08
//
[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