Alignments for a candidate for metX in Azorhizobium caulinodans ORS 571

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Azorhizobium caulinodans ORS 571

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012168760.1 AZC_RS01160 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000010525.1:WP_012168760.1
          Length = 403

 Score =  520 bits (1339), Expect = e-152
 Identities = 249/367 (67%), Positives = 300/367 (81%), Gaps = 2/367 (0%)

Query: 16  RFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPG 75
           RF A++PLRLD+G  + GL++AYQTYG+ NAD+SNA+L+CHALTGDQHVA+ +P TGKPG
Sbjct: 32  RFGADKPLRLDAGVELRGLQVAYQTYGEPNADRSNAILVCHALTGDQHVANVNPVTGKPG 91

Query: 76  WWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRA 135
           WW+ +VGPGKP+D  R F+IC+NV+GGCMG+TGP+S NPATG+ YGL  PV+TI DMV A
Sbjct: 92  WWETMVGPGKPIDTERFFVICANVLGGCMGTTGPSSTNPATGRAYGLEMPVVTIRDMVNA 151

Query: 136 QAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVG 195
           QAML+  LG+E LF V GGSMGGMQV QWA  YPER+F A+ +A+A+RHSAQNIAF EVG
Sbjct: 152 QAMLLDHLGIERLFCVAGGSMGGMQVLQWAASYPERVFCALPIATAARHSAQNIAFGEVG 211

Query: 196 RQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQRDGL-SWG 254
           RQA+MADPDWRGG Y   GV P +GL+VARMAAHITY+S+ AL RKFGR LQ   L ++G
Sbjct: 212 RQAVMADPDWRGGDYLNQGVAPHRGLSVARMAAHITYMSDQALHRKFGRRLQNRVLPTFG 271

Query: 255 FDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFC 314
           FDADFQVESYLRHQG SFV RFDANSYLY+TRAMDYFD+AA + GVLA AF R+   RFC
Sbjct: 272 FDADFQVESYLRHQGESFVQRFDANSYLYVTRAMDYFDLAADYDGVLANAF-RSSKTRFC 330

Query: 315 VLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLAS 374
           V+SF+SDWL+ T ++R +V AL A+GA  ++AEIESDKGHDAFLL+EP +     GFL S
Sbjct: 331 VVSFTSDWLFTTQDSRAIVHALNASGASVSYAEIESDKGHDAFLLEEPELFDISRGFLDS 390

Query: 375 AERDRGL 381
           A R  GL
Sbjct: 391 AARAAGL 397


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: 524
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: 403
Length adjustment: 31
Effective length of query: 351
Effective length of database: 372
Effective search space:   130572
Effective search space used:   130572
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_012168760.1 AZC_RS01160 (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.19575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-149  481.9   0.0   6.3e-149  481.8   0.0    1.0  1  lcl|NCBI__GCF_000010525.1:WP_012168760.1  AZC_RS01160 homoserine O-acetylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010525.1:WP_012168760.1  AZC_RS01160 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.8   0.0  6.3e-149  6.3e-149       2     350 ..      36     388 ..      35     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 481.8 bits;  conditional E-value: 6.3e-149
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgrald 69 
                                               +++l l++G +l+ ++vay+tyG+ na+r+Na+lvcHaltg++hva+ +  + k GWW++++Gpg+++d
  lcl|NCBI__GCF_000010525.1:WP_012168760.1  36 DKPLRLDAGVELRGLQVAYQTYGEPNADRSNAILVCHALTGDQHVANVNPVTGKpGWWETMVGPGKPID 104
                                               5899******************************************998876667************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+r+fv+c+NvlG+c G+tgP+s+np+tg+ yg e+P+vtirD+v+aq++lld+Lg+e+l++v GgS+G
  lcl|NCBI__GCF_000010525.1:WP_012168760.1 105 TERFFVICANVLGGCMGTTGPSSTNPATGRAYGLEMPVVTIRDMVNAQAMLLDHLGIERLFCVAGGSMG 173
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARm 206
                                               Gmq+l+wa+syperv  ++++at+ar+saq+iaf ev rqa+++Dp++++G+y +++ +P++GL++ARm
  lcl|NCBI__GCF_000010525.1:WP_012168760.1 174 GMQVLQWAASYPERVFCALPIATAARHSAQNIAFGEVGRQAVMADPDWRGGDYLNQGvAPHRGLSVARM 242
                                               *********************************************************9*********** PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                                a++tY s+++l+++fgr+ +++  +++ ++++f+vesylr+qg++fv+rFdAnsYl++t+a+d++dla
  lcl|NCBI__GCF_000010525.1:WP_012168760.1 243 AAHITYMSDQALHRKFGRRLQNRVLPTFGFDADFQVESYLRHQGESFVQRFDANSYLYVTRAMDYFDLA 311
                                               ********************************************************************* PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               +++++ l++a+++ k++++vv+++sD+lft+++++ +++al+a++++  yaeies++GHDaFlle+ ++
  lcl|NCBI__GCF_000010525.1:WP_012168760.1 312 ADYDGVLANAFRSSKTRFCVVSFTSDWLFTTQDSRAIVHALNASGASvsYAEIESDKGHDAFLLEEPEL 380
                                               *******************************************999999*****************998 PP

                                 TIGR01392 343 eelirefl 350
                                                ++ r fl
  lcl|NCBI__GCF_000010525.1:WP_012168760.1 381 FDISRGFL 388
                                               88777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (403 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: 7.79
//
[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