Alignments for a candidate for metX in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Azospirillum brasilense Sp245

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate AZOBR_RS20475 AZOBR_RS20475 homoserine acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>FitnessBrowser__azobra:AZOBR_RS20475
          Length = 394

 Score =  514 bits (1325), Expect = e-150
 Identities = 250/367 (68%), Positives = 291/367 (79%), Gaps = 5/367 (1%)

Query: 20  NEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGWWQR 79
           + P+RLDSG  +   E+AYQTYG LNAD+SNA+LICHALTGD +V   HP TGKPGWW+ 
Sbjct: 22  DRPMRLDSGAELGPFEVAYQTYGALNADRSNAILICHALTGDHYVLDQHPVTGKPGWWEM 81

Query: 80  LVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAML 139
           LVGPGKP+D  R+F+ICSNVIGGCMGSTGP   +PATG+ YGL FPVITI DMVRAQ +L
Sbjct: 82  LVGPGKPVDTDRYFVICSNVIGGCMGSTGPKETDPATGEPYGLGFPVITIGDMVRAQKLL 141

Query: 140 VSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQAI 199
           V  LG++ LF V+GGSMGGMQV QWAV YPE +F+AV +A+A+RHSAQNIAFHEVGRQAI
Sbjct: 142 VEHLGIDQLFCVIGGSMGGMQVLQWAVAYPESVFAAVPIATAARHSAQNIAFHEVGRQAI 201

Query: 200 MADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGFDAD 258
           MADPDW GG Y   G RP +GLAVARMAAHITYLSEPAL RKFGR LQ R  +++GFDAD
Sbjct: 202 MADPDWAGGNYLLEGTRPHRGLAVARMAAHITYLSEPALHRKFGRNLQNRQTVTYGFDAD 261

Query: 259 FQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASH-GGVLAKAFT---RARNVRFC 314
           FQVESYLRHQG +FV+RFDANSYLYITRAMDYFD+AA + GG L+ AF    +   VRFC
Sbjct: 262 FQVESYLRHQGITFVERFDANSYLYITRAMDYFDLAADYGGGTLSNAFRKDGKGTPVRFC 321

Query: 315 VLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLAS 374
           + SFSSDWL+PT+E+R +V AL A  A  +F EI +DKGHD+FLLDEP     + GFL  
Sbjct: 322 LASFSSDWLFPTSESRAIVHALNAVAANVSFVEIRTDKGHDSFLLDEPEFHQVIRGFLDG 381

Query: 375 AERDRGL 381
               RGL
Sbjct: 382 CAEHRGL 388


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: 585
Number of extensions: 25
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: 394
Length adjustment: 30
Effective length of query: 352
Effective length of database: 364
Effective search space:   128128
Effective search space used:   128128
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 AZOBR_RS20475 AZOBR_RS20475 (homoserine 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.23033.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-145  470.0   0.0   2.6e-145  469.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS20475  AZOBR_RS20475 homoserine acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS20475  AZOBR_RS20475 homoserine acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.8   0.0  2.6e-145  2.6e-145       3     350 ..      23     379 ..      21     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 469.8 bits;  conditional E-value: 2.6e-145
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               +++ l+sG++l  +evay+tyG lna+r+Na+l+cHaltg++ v +++  + k GWW+ l+Gpg+++dt
  lcl|FitnessBrowser__azobra:AZOBR_RS20475  23 RPMRLDSGAELGPFEVAYQTYGALNADRSNAILICHALTGDHYVLDQHPVTGKpGWWEMLVGPGKPVDT 91 
                                               5789*****************************************999877667*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +ryfv+c+Nv+G+c GstgP  ++p+tg+pyg  fP++ti D+v+aqk l+++Lg+++l++v+GgS+GG
  lcl|FitnessBrowser__azobra:AZOBR_RS20475  92 DRYFVICSNVIGGCMGSTGPKETDPATGEPYGLGFPVITIGDMVRAQKLLVEHLGIDQLFCVIGGSMGG 160
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+l+wa++ype+v ++v++at+ar+saq+iaf+ev rqai++Dp++ +G+y  e+ +P++GLa+ARm 
  lcl|FitnessBrowser__azobra:AZOBR_RS20475 161 MQVLQWAVAYPESVFAAVPIATAARHSAQNIAFHEVGRQAIMADPDWAGGNYLLEGtRPHRGLAVARMA 229
                                               *****************************************************9999************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276
                                               a++tY+se +l+++fgr+ ++++++++ ++++f+vesylr+qg +fverFdAnsYl++t+a+d++dla+
  lcl|FitnessBrowser__azobra:AZOBR_RS20475 230 AHITYLSEPALHRKFGRNLQNRQTVTYGFDADFQVESYLRHQGITFVERFDANSYLYITRAMDYFDLAA 298
                                               ********************************************************************* PP

                                 TIGR01392 277 gr.rdslkealkk....ikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFlle 338
                                               ++  + l++a++k    + +++++++++sD+lf+++e++ +++al+a++++  ++ei++++GHD+Fll+
  lcl|FitnessBrowser__azobra:AZOBR_RS20475 299 DYgGGTLSNAFRKdgkgTPVRFCLASFSSDWLFPTSESRAIVHALNAVAANvsFVEIRTDKGHDSFLLD 367
                                               *96678999*97644447899*************************9998888**************** PP

                                 TIGR01392 339 kekveelirefl 350
                                               + +++++ir fl
  lcl|FitnessBrowser__azobra:AZOBR_RS20475 368 EPEFHQVIRGFL 379
                                               *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (394 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: 11.83
//
[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