Alignments for a candidate for metX in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Sulfurivirga caldicuralii DSM 17737

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_074201658.1 BUQ81_RS06945 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_900141795.1:WP_074201658.1
          Length = 378

 Score =  395 bits (1014), Expect = e-114
 Identities = 199/366 (54%), Positives = 255/366 (69%), Gaps = 4/366 (1%)

Query: 17  FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76
           F  +EPL   SG VI   ++ Y+TYGQLNADKSNA+LICHAL+G+ HVA  +    KPGW
Sbjct: 14  FHVDEPLHTVSGSVIPAYDLVYETYGQLNADKSNAILICHALSGNHHVAGYYDGDEKPGW 73

Query: 77  WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136
           W+  VGPGKP+D  R F++  N +GGC GSTGPASINP TG+ +G  FP+IT+ D V +Q
Sbjct: 74  WEHYVGPGKPIDTNRFFVVGVNNLGGCHGSTGPASINPETGRPWGPDFPIITVKDWVVSQ 133

Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196
             L   LG+E   AVVGGS+GGMQV QWA+D P+R+  AVV+A+A R SAQNIAF+EV R
Sbjct: 134 DKLREHLGIEQWAAVVGGSLGGMQVIQWAIDRPDRLRHAVVIAAAPRLSAQNIAFNEVAR 193

Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQRDGLSWGFD 256
            AIM+DPD+ GG Y EHGV P++GLA+ARM  H+TYLS+  + +KFGREL RD L + FD
Sbjct: 194 TAIMSDPDFHGGRYLEHGVIPKRGLALARMLGHLTYLSDDLMGKKFGREL-RDRLKYNFD 252

Query: 257 ADFQVESYLRHQGSSFVDR--FDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFC 314
            +FQVESYLR+QG  F  R  FDAN+YL +T+A+DYFD AA +   L+KAF R +   F 
Sbjct: 253 VEFQVESYLRYQGEKFATRSKFDANTYLLMTKALDYFDPAAEYDHDLSKAFARVQ-AGFL 311

Query: 315 VLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLAS 374
           V+SF+SDW +    +  +VRAL       ++AEIES  GHDAFLL  P  +     ++  
Sbjct: 312 VVSFTSDWRFSPERSEEIVRALLDNDKNVSYAEIESQHGHDAFLLPNPFYEGVFSAYMDR 371

Query: 375 AERDRG 380
             R+ G
Sbjct: 372 VAREVG 377


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: 446
Number of extensions: 22
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: 382
Length of database: 378
Length adjustment: 30
Effective length of query: 352
Effective length of database: 348
Effective search space:   122496
Effective search space used:   122496
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_074201658.1 BUQ81_RS06945 (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.16198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-143  464.1   0.0   1.6e-143  464.0   0.0    1.0  1  lcl|NCBI__GCF_900141795.1:WP_074201658.1  BUQ81_RS06945 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900141795.1:WP_074201658.1  BUQ81_RS06945 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.0   0.0  1.6e-143  1.6e-143       3     345 ..      18     364 ..      16     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.0 bits;  conditional E-value: 1.6e-143
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               e+l++ sG+v++ ++++y+tyG+lna+++Na+l+cHal+g++hvag++d ++k GWW++++Gpg+++dt
  lcl|NCBI__GCF_900141795.1:WP_074201658.1  18 EPLHTVSGSVIPAYDLVYETYGQLNADKSNAILICHALSGNHHVAGYYDGDEKpGWWEHYVGPGKPIDT 86 
                                               789999*******************************************98888*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +r+fvv++N+lG+c+GstgP+sinpetg+p+g++fP +t++D+v  q +l ++Lg+e++aavvGgSlGG
  lcl|NCBI__GCF_900141795.1:WP_074201658.1  87 NRFFVVGVNNLGGCHGSTGPASINPETGRPWGPDFPIITVKDWVVSQDKLREHLGIEQWAAVVGGSLGG 155
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+++wa++ p+r++++vv+a+++r+saq+iafnev+r ai+sDp++++G+y e++  P++GLalARml
  lcl|NCBI__GCF_900141795.1:WP_074201658.1 156 MQVIQWAIDRPDRLRHAVVIAAAPRLSAQNIAFNEVARTAIMSDPDFHGGRYLEHGvIPKRGLALARML 224
                                               ********************************************************9************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfver..FdAnsYllltkaldthdl 274
                                               ++ltY+s++ + ++fgre +++  l+++++ ef+vesylryqg+kf++r  FdAn+Yll+tkald++d 
  lcl|NCBI__GCF_900141795.1:WP_074201658.1 225 GHLTYLSDDLMGKKFGRELRDR--LKYNFDVEFQVESYLRYQGEKFATRskFDANTYLLMTKALDYFDP 291
                                               ******************9999..67888*****************97555****************** PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                               a++++++l++a+++++a +lvv+++sD++f++e++ee+++al +++++  yaeies++GHDaFll +  
  lcl|NCBI__GCF_900141795.1:WP_074201658.1 292 AAEYDHDLSKAFARVQAGFLVVSFTSDWRFSPERSEEIVRALLDNDKNvsYAEIESQHGHDAFLLPNPF 360
                                               ******************************************99999889**************98877 PP

                                 TIGR01392 342 veel 345
                                               +e +
  lcl|NCBI__GCF_900141795.1:WP_074201658.1 361 YEGV 364
                                               6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (378 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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