Alignments for a candidate for metX in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Methylocystis bryophila S285

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_085773694.1 B1812_RS12585 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_002117405.1:WP_085773694.1
          Length = 386

 Score =  508 bits (1308), Expect = e-148
 Identities = 249/373 (66%), Positives = 293/373 (78%), Gaps = 2/373 (0%)

Query: 10  AGGGTWRFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHP 69
           + G    FP  +PL  D G VI  L IAY+TYG LN  K+NA+L+CHALTGDQ+ A  HP
Sbjct: 9   SNGKRVHFPPEKPLVTDGGRVIAPLTIAYETYGALNEAKNNAILLCHALTGDQYAAGVHP 68

Query: 70  TTGKPGWWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITI 129
            TGKPGWW  LVGPG+P D  R FII +NV+GGCMG+TGPASIN AT + +GL FPV+TI
Sbjct: 69  VTGKPGWWDVLVGPGRPFDTNRFFIISTNVVGGCMGTTGPASINLATARPFGLDFPVVTI 128

Query: 130 ADMVRAQAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNI 189
            DMVRAQAML+  LG+ETLF V GGSMGGMQV QWA  YPER+F+A+ +A+A RHS+QNI
Sbjct: 129 RDMVRAQAMLIDHLGIETLFCVAGGSMGGMQVLQWAASYPERVFAAMPIATAPRHSSQNI 188

Query: 190 AFHEVGRQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-R 248
           AFHEVGRQA+MADPDWR G Y E GVRPEKGLAVARMAAHITYLSE ALQRKFGR+LQ R
Sbjct: 189 AFHEVGRQAVMADPDWRAGRYLEAGVRPEKGLAVARMAAHITYLSEQALQRKFGRKLQDR 248

Query: 249 DGLSWGFDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRA 308
              ++ FDADFQ+ESYLR+QG +FV+RFDANSYL++TRA DYFD+AA +GG LA AF + 
Sbjct: 249 AAPTFSFDADFQIESYLRYQGLAFVERFDANSYLFVTRACDYFDLAADYGGSLALAF-KG 307

Query: 309 RNVRFCVLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAAL 368
              RFCV+SF+SDWLYPT+++R +V AL A GA  +F EIESDKGHDAFLL EP   A  
Sbjct: 308 SKTRFCVISFTSDWLYPTSDSRAIVHALNAGGASVSFVEIESDKGHDAFLLYEPDFFATT 367

Query: 369 EGFLASAERDRGL 381
            GFL +A   RG+
Sbjct: 368 RGFLEAAANARGI 380


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: 484
Number of extensions: 18
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: 386
Length adjustment: 30
Effective length of query: 352
Effective length of database: 356
Effective search space:   125312
Effective search space used:   125312
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_085773694.1 B1812_RS12585 (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.19058.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-143  462.0   0.0   7.4e-143  461.8   0.0    1.0  1  lcl|NCBI__GCF_002117405.1:WP_085773694.1  B1812_RS12585 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085773694.1  B1812_RS12585 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.8   0.0  7.4e-143  7.4e-143       3     350 ..      20     371 ..      18     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 461.8 bits;  conditional E-value: 7.4e-143
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               ++l+++ G v+  +++ay+tyG ln++++Na+l+cHaltg++ +ag +  + k GWWd l+Gpgr++dt
  lcl|NCBI__GCF_002117405.1:WP_085773694.1  20 KPLVTDGGRVIAPLTIAYETYGALNEAKNNAILLCHALTGDQYAAGVHPVTGKpGWWDVLVGPGRPFDT 88 
                                               78999*****************************************99987767*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +r+f++++Nv+G+c G+tgP+sin +t +p+g +fP+vtirD+v+aq++l+d+Lg+e+l++v GgS+GG
  lcl|NCBI__GCF_002117405.1:WP_085773694.1  89 NRFFIISTNVVGGCMGTTGPASINLATARPFGLDFPVVTIRDMVRAQAMLIDHLGIETLFCVAGGSMGG 157
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+l+wa+syperv +++++at++r+s+q+iaf+ev rqa+++Dp+++ G+y e + +PekGLa+ARm 
  lcl|NCBI__GCF_002117405.1:WP_085773694.1 158 MQVLQWAASYPERVFAAMPIATAPRHSSQNIAFHEVGRQAVMADPDWRAGRYLEAGvRPEKGLAVARMA 226
                                               ********************************************************************* PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276
                                               a++tY+se++l+++fgr+ ++++++++s++++f++esylryqg  fverFdAnsYl +t+a d++dla+
  lcl|NCBI__GCF_002117405.1:WP_085773694.1 227 AHITYLSEQALQRKFGRKLQDRAAPTFSFDADFQIESYLRYQGLAFVERFDANSYLFVTRACDYFDLAA 295
                                               ********************************************************************* PP

                                 TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343
                                               ++ +sl+ a+k  k++++v++++sD+l+++++++ +++al+a +++  ++eies++GHDaFll +  + 
  lcl|NCBI__GCF_002117405.1:WP_085773694.1 296 DYGGSLALAFKGSKTRFCVISFTSDWLYPTSDSRAIVHALNAGGASvsFVEIESDKGHDAFLLYEPDFF 364
                                               *****************************************9998888***************998887 PP

                                 TIGR01392 344 elirefl 350
                                               ++ r fl
  lcl|NCBI__GCF_002117405.1:WP_085773694.1 365 ATTRGFL 371
                                               7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (386 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.59
//
[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