Alignments for a candidate for metX in Methylocapsa aurea KYG T

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Methylocapsa aurea KYG T

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_036257153.1 DL86_RS00085 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000746085.1:WP_036257153.1
          Length = 397

 Score =  505 bits (1300), Expect = e-147
 Identities = 243/366 (66%), Positives = 295/366 (80%), Gaps = 2/366 (0%)

Query: 17  FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76
           F A  PL++D+G     L IAYQTYG LNADKSNAVL+CHALTGDQHVA+ HP TGKPGW
Sbjct: 25  FGAEHPLQMDAGISFSPLTIAYQTYGALNADKSNAVLVCHALTGDQHVANDHPITGKPGW 84

Query: 77  WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136
           WQ +VGPG+P+D  R+F+I SNV+GGCMG+TGPAS+NP TG+ YGL  P++TI DMVRAQ
Sbjct: 85  WQTMVGPGRPIDTDRYFVISSNVVGGCMGTTGPASLNPTTGRPYGLDLPIVTIRDMVRAQ 144

Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196
           AML+  LG++T+F VVGGSMGGMQV QW   + ER+F+A+ +A+A++HS+QNIAFHEVGR
Sbjct: 145 AMLIDHLGIDTIFCVVGGSMGGMQVLQWVASFQERVFAAMPIATAAKHSSQNIAFHEVGR 204

Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGF 255
           QA+MADPDWR G Y E GV P KGLAVARMAAHITYLS+ ALQ KFGR+LQ R   ++ F
Sbjct: 205 QAVMADPDWRRGRYLEEGVIPTKGLAVARMAAHITYLSDEALQSKFGRKLQGRVAPTFSF 264

Query: 256 DADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCV 315
           DA+FQ+E+YLR+QG SFVDRFDANSYLY+TRA DYFD+AA + G LA AF  A+  RFCV
Sbjct: 265 DAEFQIENYLRYQGMSFVDRFDANSYLYVTRACDYFDLAADYDGSLALAFKGAK-TRFCV 323

Query: 316 LSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASA 375
           +SF+SDWLYPTA +R +V AL A GA  +F +IE+D+GHDAFLL+ P   A   GFL +A
Sbjct: 324 VSFNSDWLYPTAASRAIVHALNAGGASVSFVDIETDRGHDAFLLNIPEFIATSRGFLDAA 383

Query: 376 ERDRGL 381
            R RGL
Sbjct: 384 ARARGL 389


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: 486
Number of extensions: 16
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: 397
Length adjustment: 30
Effective length of query: 352
Effective length of database: 367
Effective search space:   129184
Effective search space used:   129184
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_036257153.1 DL86_RS00085 (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.19230.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-143  461.5   0.0     1e-142  461.3   0.0    1.0  1  lcl|NCBI__GCF_000746085.1:WP_036257153.1  DL86_RS00085 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000746085.1:WP_036257153.1  DL86_RS00085 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.3   0.0    1e-142    1e-142       2     347 ..      28     377 ..      27     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 461.3 bits;  conditional E-value: 1e-142
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgrald 69 
                                               e++l++++G   s +++ay+tyG lna+++NavlvcHaltg++hva+ +  + k GWW++++Gpgr++d
  lcl|NCBI__GCF_000746085.1:WP_036257153.1  28 EHPLQMDAGISFSPLTIAYQTYGALNADKSNAVLVCHALTGDQHVANDHPITGKpGWWQTMVGPGRPID 96 
                                               5789******************************************988866556************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+ryfv+++Nv+G+c G+tgP+s+np+tg+pyg ++P vtirD+v+aq++l+d+Lg++++++vvGgS+G
  lcl|NCBI__GCF_000746085.1:WP_036257153.1  97 TDRYFVISSNVVGGCMGTTGPASLNPTTGRPYGLDLPIVTIRDMVRAQAMLIDHLGIDTIFCVVGGSMG 165
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARm 206
                                               Gmq+l+w++s +erv +++++at+a++s+q+iaf+ev rqa+++Dp+++ G+y ee+  P+kGLa+ARm
  lcl|NCBI__GCF_000746085.1:WP_036257153.1 166 GMQVLQWVASFQERVFAAMPIATAAKHSSQNIAFHEVGRQAVMADPDWRRGRYLEEGvIPTKGLAVARM 234
                                               *********************************************************9*********** PP

                                 TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                                a++tY+s+e+l+++fgr+ + + ++++s+++ef++e ylryqg +fv+rFdAnsYl++t+a d++dla
  lcl|NCBI__GCF_000746085.1:WP_036257153.1 235 AAHITYLSDEALQSKFGRKLQGRVAPTFSFDAEFQIENYLRYQGMSFVDRFDANSYLYVTRACDYFDLA 303
                                               ********************************************************************* PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               +++++sl+ a+k +k++++vv+++sD+l++++ ++ +++al+a +++  ++ ie+++GHDaFll+  ++
  lcl|NCBI__GCF_000746085.1:WP_036257153.1 304 ADYDGSLALAFKGAKTRFCVVSFNSDWLYPTAASRAIVHALNAGGASvsFVDIETDRGHDAFLLNIPEF 372
                                               ******************************************9998888***************99887 PP

                                 TIGR01392 343 eelir 347
                                                ++ r
  lcl|NCBI__GCF_000746085.1:WP_036257153.1 373 IATSR 377
                                               66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (397 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: 8.95
//
[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