Alignments for a candidate for thrC in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Trichormus variabilis ATCC 29413

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011319854.1 AVA_RS15760 threonine synthase

Query= BRENDA::O66740
         (352 letters)



>NCBI__GCF_000204075.1:WP_011319854.1
          Length = 363

 Score =  438 bits (1127), Expect = e-128
 Identities = 216/351 (61%), Positives = 271/351 (77%), Gaps = 4/351 (1%)

Query: 4   WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63
           W G+I+ Y++YLPV E TP+VTL EGNTPLI    +A  IG +  +++KY+GLNPTGSFK
Sbjct: 15  WPGLIEAYREYLPVSEQTPVVTLLEGNTPLIPVPAIAERIGRQVSVFVKYDGLNPTGSFK 74

Query: 64  DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123
           DRGMT+AISKA EAG +AVICASTGNTSA+AAAYA R G++A+VL+P G VA+GKL+QA+
Sbjct: 75  DRGMTMAISKAKEAGAKAVICASTGNTSAAAAAYARRGGMKAFVLIPDGYVALGKLAQAL 134

Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183
           +YGA+VLAI+G FD AL IVR++ E +P+ +VNSVNPYR+EGQKT AFE+ D LG APD+
Sbjct: 135 LYGAEVLAIKGNFDRALEIVREMAETYPITLVNSVNPYRLEGQKTGAFEVVDALGNAPDW 194

Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAI 243
             IPVGNAGNITAYW GF  Y++ GK  +LP+MMG+QA GAAP+V G P+ +P+TIATAI
Sbjct: 195 LCIPVGNAGNITAYWMGFCQYHQAGKCDRLPQMMGFQAAGAAPLVNGQPVSHPETIATAI 254

Query: 244 KIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLV 303
           +IGNP SW  A+ A   S G  +AV+D EIL AY+L+AS+EG+FCEPASAASVAGL+K+ 
Sbjct: 255 RIGNPASWDKAIAAQSASQGSFNAVTDEEILDAYRLLASSEGIFCEPASAASVAGLLKVK 314

Query: 304 REGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPIT--VPPDFDEVVKVLGF 352
            +     G  V C LTGNGLKDPDTAIK         +  D  +V K +GF
Sbjct: 315 DQ--VPTGATVVCVLTGNGLKDPDTAIKHSHSQFKQGLEADLKDVAKAMGF 363


Lambda     K      H
   0.317    0.136    0.400 

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: 472
Number of extensions: 15
Number of successful extensions: 2
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: 352
Length of database: 363
Length adjustment: 29
Effective length of query: 323
Effective length of database: 334
Effective search space:   107882
Effective search space used:   107882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_011319854.1 AVA_RS15760 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.30617.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-107  345.1   0.0   2.6e-107  344.9   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011319854.1  AVA_RS15760 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319854.1  AVA_RS15760 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.9   0.0  2.6e-107  2.6e-107       1     340 []      19     336 ..      19     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 344.9 bits;  conditional E-value: 2.6e-107
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 
                                               ++ yre+l+v+ ++++v+l eg+t+l+ +p++ae++g    ++vk ++++Pt++FKDrg   ++++++k
  lcl|NCBI__GCF_000204075.1:WP_011319854.1  19 IEAYREYLPVSeQTPVVTLLEGNTPLIPVPAIAERIGRqVSVFVKYDGLNPTGSFKDRG---MTMAISK 84 
                                               678***********************************99*******************...******* PP

                                 TIGR00260  68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136
                                               a+e+g+++v+cA++G+t+aaaa a+a++ ++k++vL+P+g+++   +kl++al ++a+vlaikG+FD a
  lcl|NCBI__GCF_000204075.1:WP_011319854.1  85 AKEAGAKAVICASTGNTSAAAA-AYARRGGMKAFVLIPDGYVA--LGKLAQALLYGAEVLAIKGNFDRA 150
                                               **********************.********************..************************ PP

                                 TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204
                                               +++v+e++e  +++++nsvN   p+r+e+qkt afe+v++lg ++pd++++pv+ +gn++a+++Gf+++
  lcl|NCBI__GCF_000204075.1:WP_011319854.1 151 LEIVREMAETYPITLVNSVN---PYRLEGQKTGAFEVVDALG-NAPDWLCIPVGnAGNITAYWMGFCQY 215
                                               ********999999999999...*******************.************************** PP

                                 TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269
                                               +++g    lp ++++++a gaa+ v+ +       p +++eT++tA++ignp+++++a ++   s+g +
  lcl|NCBI__GCF_000204075.1:WP_011319854.1 216 HQAGkcdrLP-QMMGFQAAGAAPLVNGQ-------PVSHPETIATAIRIGNPASWDKAIAAQSASQGSF 276
                                               **********.************99988.......9********************************* PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338
                                               +++    +deeil+a+++la +eg+++ep++a++va+l+k  +     +++ +  ++vv++ltgn+lkd
  lcl|NCBI__GCF_000204075.1:WP_011319854.1 277 NAV----TDEEILDAYRLLASSEGIFCEPASAASVAGLLKVKD-----QVPTG--ATVVCVLTGNGLKD 334
                                               ***....*********************************987.....7899*..************** PP

                                 TIGR00260 339 pe 340
                                               p+
  lcl|NCBI__GCF_000204075.1:WP_011319854.1 335 PD 336
                                               97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (363 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.50
//
[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