Alignments for a candidate for metX in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Burkholderia phytofirmans PsJN

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate BPHYT_RS01595 BPHYT_RS01595 homoserine O-acetyltransferase

Query= SwissProt::Q12XS2
         (488 letters)



>FitnessBrowser__BFirm:BPHYT_RS01595
          Length = 381

 Score =  360 bits (924), Expect = e-104
 Identities = 179/369 (48%), Positives = 243/369 (65%), Gaps = 7/369 (1%)

Query: 5   SVGIVATNYHTIEGEFQLEGGHTLKNIRLAYETYGNLNKEKSNAILVCHALTGDAHAAGR 64
           S+GIVA +        QL+ G +L    L  ETYG LN  +SNA+LVCHAL    H AG 
Sbjct: 3   SIGIVAPHKMHFTEPLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGV 62

Query: 65  HSDDDKKPGWWDDIIGPGKALDTDRYFVLCSNVLGGCKGTTGPASLDPDTGRQYGITFPV 124
           ++D+ K  GWWD+++GPGK LDTD++FV+  N LG C G+TGP S+DP TG  YG  FPV
Sbjct: 63  YADNPKDIGWWDNMVGPGKPLDTDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPV 122

Query: 125 ITIRDMVNVQKRLIDHMGITTLFAVVGGSMGGMQTLQWCVAYPELVKKAVVIASTAVSSP 184
           +T+ D VN Q R+ D  GIT   AV+GGS+GGMQ L W + YPE V   +V+AST   S 
Sbjct: 123 VTVEDWVNAQARVADQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKLSA 182

Query: 185 QQIAFNEVGRNAIISDPDWNGGDYY-EGEPPVNGLSTARMIAHITYLSDASMHEKFGRRL 243
           Q IAFNEV R+AI+SDPD++GG+YY     P  GL  ARMI HITYLSD  M EKFGR L
Sbjct: 183 QNIAFNEVARSAILSDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGRSL 242

Query: 244 QQGE----SYKFDMSNDFQVGSYLKYQGDTFTGRFDANSYLYATKAVDYFD--LSMNGSL 297
           ++ E    +Y F+   +F+V SYL+YQGD F   FDAN+YL  T+A+DYFD   + +G L
Sbjct: 243 RRAEGAVDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFDGDL 302

Query: 298 AEGLKYVQAKMLVISITSDWLYSPYHSKKIVEGLTVKEHDVSYREIESSYGHDAFLLESG 357
              + +  AK L+ S ++DW ++P  S+++V+ L   +  V+Y EI++ +GHDAFLL+  
Sbjct: 303 TAAVAHTTAKYLIASFSTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLDDA 362

Query: 358 QINYVIHNF 366
           + + ++  +
Sbjct: 363 RYHNLMRAY 371


Lambda     K      H
   0.318    0.134    0.397 

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: 528
Number of extensions: 28
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: 488
Length of database: 381
Length adjustment: 32
Effective length of query: 456
Effective length of database: 349
Effective search space:   159144
Effective search space used:   159144
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 BPHYT_RS01595 BPHYT_RS01595 (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.28610.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.1e-143  463.0   0.1   3.5e-143  462.8   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  BPHYT_RS01595 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS01595  BPHYT_RS01595 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.8   0.1  3.5e-143  3.5e-143       2     349 ..      15     371 ..      14     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 462.8 bits;  conditional E-value: 3.5e-143
                                TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                              +e+l+l++G+ l  ++++++tyGtlna+r+NavlvcHal +s+hvag + ++ k  GWWd+++Gpg++ld
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  15 TEPLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYADNPKdiGWWDNMVGPGKPLD 84 
                                              579**********************************************9888899************** PP

                                TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                              t+++fv+++N+lGsc GstgP+si+p+tg+pyga fP+vt++D+v+aq++++d++g++++aav+GgSlGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  85 TDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPVVTVEDWVNAQARVADQFGITRFAAVMGGSLGG 154
                                              ********************************************************************** PP

                                TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmla 208
                                              mqal w+++yperv +++v+a+++++saq+iafnev+r ailsDp++++G+y+ ++ +P++GL++ARm++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 155 MQALAWSMMYPERVGHCIVVASTPKLSAQNIAFNEVARSAILSDPDFHGGNYYAHNvKPKRGLRVARMIG 224
                                              *******************************************************99************* PP

                                TIGR01392 209 lltYrseesleerfgreaksee....slassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                              ++tY+s+++++e+fgr+ +++e    +++++++ ef+vesylryqg+kf++ FdAn+Yll+t+ald++d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 225 HITYLSDDDMAEKFGRSLRRAEgavdAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDP 294
                                              *****************999984444444556************************************** PP

                                TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                              a+  +++l++a+++++a++l++++++D++f++++++el+kal + k +  yaei+ ++GHDaFll+++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 295 AKAFDGDLTAAVAHTTAKYLIASFSTDWRFAPARSRELVKALLDHKRTvtYAEIDAPHGHDAFLLDDARY 364
                                              ******************************************98888778******************** PP

                                TIGR01392 343 eeliref 349
                                              ++l+r++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 365 HNLMRAY 371
                                              *999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (381 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.84
//
[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