Alignments for a candidate for metX in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Bradyrhizobium sp. BTAi1

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_041750362.1 BBTA_RS05605 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000015165.1:WP_041750362.1
          Length = 404

 Score =  533 bits (1372), Expect = e-156
 Identities = 259/367 (70%), Positives = 305/367 (83%), Gaps = 2/367 (0%)

Query: 16  RFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPG 75
           +F A++PL+LD G  +   +IAYQTYG+LNADKSNAVLICHALTGDQHVA+ HP TGKPG
Sbjct: 33  QFGADKPLKLDCGVDLSPFQIAYQTYGELNADKSNAVLICHALTGDQHVANRHPVTGKPG 92

Query: 76  WWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRA 135
           WW+ LVG G+PLDP+R+FI+CSNVIGGCMGSTGPAS+NPATGK +GL FP+ITI DMVRA
Sbjct: 93  WWETLVGKGRPLDPSRYFIVCSNVIGGCMGSTGPASLNPATGKVWGLDFPIITIPDMVRA 152

Query: 136 QAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVG 195
           QAML+  LG++TLFAVVGGSMGGMQ  QW V YP+R+F+ + +A A+RHSAQNIAFHE+G
Sbjct: 153 QAMLIDHLGIDTLFAVVGGSMGGMQALQWTVAYPQRVFATLAIACATRHSAQNIAFHELG 212

Query: 196 RQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWG 254
           RQA+MADPDW  G Y + GV P +GLAVARMAAHITYLS+ AL RKFGR +Q R+  ++ 
Sbjct: 213 RQAVMADPDWDHGRYGDKGVHPHRGLAVARMAAHITYLSDAALHRKFGRRMQDRELPTFS 272

Query: 255 FDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFC 314
           FDADFQVESYLR+QGSSFV+RFDANSYLY+TRAMDYFDIAA H GVLA AF R    RFC
Sbjct: 273 FDADFQVESYLRYQGSSFVERFDANSYLYLTRAMDYFDIAADHDGVLAAAF-RGIKTRFC 331

Query: 315 VLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLAS 374
           V+SF+SDWL+PT+E+R LV AL A+ AR +FAEIE+DKGHDAFLLD P        FL S
Sbjct: 332 VVSFTSDWLFPTSESRALVHALNASSARVSFAEIETDKGHDAFLLDVPEFFDIASAFLDS 391

Query: 375 AERDRGL 381
           A + RGL
Sbjct: 392 AGKARGL 398


Lambda     K      H
   0.321    0.135    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: 548
Number of extensions: 27
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: 382
Length of database: 404
Length adjustment: 31
Effective length of query: 351
Effective length of database: 373
Effective search space:   130923
Effective search space used:   130923
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_041750362.1 BBTA_RS05605 (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.25394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-151  489.6   0.0   2.9e-151  489.4   0.0    1.0  1  lcl|NCBI__GCF_000015165.1:WP_041750362.1  BBTA_RS05605 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_041750362.1  BBTA_RS05605 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.4   0.0  2.9e-151  2.9e-151       2     350 ..      37     389 ..      36     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 489.4 bits;  conditional E-value: 2.9e-151
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgrald 69 
                                               +++l+l++G  ls +++ay+tyG+lna+++Navl+cHaltg++hva+++  + k GWW++l+G+gr+ld
  lcl|NCBI__GCF_000015165.1:WP_041750362.1  37 DKPLKLDCGVDLSPFQIAYQTYGELNADKSNAVLICHALTGDQHVANRHPVTGKpGWWETLVGKGRPLD 105
                                               689*********************************************9987767************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               +sryf+vc+Nv+G+c GstgP+s+np+tgk +g +fP +ti D+v+aq++l+d+Lg+++l+avvGgS+G
  lcl|NCBI__GCF_000015165.1:WP_041750362.1 106 PSRYFIVCSNVIGGCMGSTGPASLNPATGKVWGLDFPIITIPDMVRAQAMLIDHLGIDTLFAVVGGSMG 174
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARm 206
                                               Gmqal+w+++yp+rv +++++a ++r+saq+iaf+e+ rqa+++Dp++ +G+y +++ +P++GLa+ARm
  lcl|NCBI__GCF_000015165.1:WP_041750362.1 175 GMQALQWTVAYPQRVFATLAIACATRHSAQNIAFHELGRQAVMADPDWDHGRYGDKGvHPHRGLAVARM 243
                                               ********************************************************************* PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                                a++tY+s+++l+++fgr+++++e +++s++++f+vesylryqg++fverFdAnsYl+lt+a+d++d+a
  lcl|NCBI__GCF_000015165.1:WP_041750362.1 244 AAHITYLSDAALHRKFGRRMQDRELPTFSFDADFQVESYLRYQGSSFVERFDANSYLYLTRAMDYFDIA 312
                                               ********************************************************************* PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               +++++ l++a++ ik++++vv+++sD+lf+++e++ l++al+a++++  +aeie+++GHDaFll+  ++
  lcl|NCBI__GCF_000015165.1:WP_041750362.1 313 ADHDGVLAAAFRGIKTRFCVVSFTSDWLFPTSESRALVHALNASSARvsFAEIETDKGHDAFLLDVPEF 381
                                               *******************************************999999*****************999 PP

                                 TIGR01392 343 eelirefl 350
                                                ++ ++fl
  lcl|NCBI__GCF_000015165.1:WP_041750362.1 382 FDIASAFL 389
                                               88877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (404 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: 8.31
//
[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