Alignments for a candidate for thrC in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Mycolicibacterium vanbaalenii PYR-1

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011781502.1 MVAN_RS21820 threonine synthase

Query= BRENDA::P9WG59
         (360 letters)



>NCBI__GCF_000015305.1:WP_011781502.1
          Length = 359

 Score =  618 bits (1593), Expect = 0.0
 Identities = 305/353 (86%), Positives = 329/353 (93%)

Query: 7   ATHQPWPGVIAAYRDRLPVGDDWTPVTLLEGGTPLIAATNLSKQTGCTIHLKVEGLNPTG 66
           A HQPWPG+I AYRDRLP+ D WT +TL EGGTPL+ A  LS+ TGCT+HLKVEGLNPTG
Sbjct: 6   AVHQPWPGLIEAYRDRLPIEDSWTTITLREGGTPLLPAPRLSEYTGCTVHLKVEGLNPTG 65

Query: 67  SFKDRGMTMAVTDALAHGQRAVLCASTGNTSASAAAYAARAGITCAVLIPQGKIAMGKLA 126
           SFKDRGMTMAVT+A++ GQ+AVLCASTGNTSASAAAYAARAGITCAVL+PQGKIAMGKLA
Sbjct: 66  SFKDRGMTMAVTEAVSRGQQAVLCASTGNTSASAAAYAARAGITCAVLVPQGKIAMGKLA 125

Query: 127 QAVMHGAKIIQIDGNFDDCLELARKMAADFPTISLVNSVNPVRIEGQKTAAFEIVDVLGT 186
           QAVMHGAKIIQIDGNFDDCLELARK+ +DFPT+SLVNSVNP RIEGQKTAAFEIVD LG 
Sbjct: 126 QAVMHGAKIIQIDGNFDDCLELARKLTSDFPTVSLVNSVNPFRIEGQKTAAFEIVDALGD 185

Query: 187 APDVHALPVGNAGNITAYWKGYTEYHQLGLIDKLPRMLGTQAAGAAPLVLGEPVSHPETI 246
           APDVH+LPVGNAGNITAYWKGYTEYH+ GL  +LPRMLGTQAAGAAPLVLGEPVS PETI
Sbjct: 186 APDVHSLPVGNAGNITAYWKGYTEYHRDGLAARLPRMLGTQAAGAAPLVLGEPVSDPETI 245

Query: 247 ATAIRIGSPASWTSAVEAQQQSKGRFLAASDEEILAAYHLVARVEGVFVEPASAASIAGL 306
           ATAIRIGSPASW+SAVEAQQQS GRF+AA+DEEILAAYHLVAR EGVFVEPASAASIAGL
Sbjct: 246 ATAIRIGSPASWSSAVEAQQQSGGRFVAATDEEILAAYHLVARAEGVFVEPASAASIAGL 305

Query: 307 LKAIDDGWVARGSTVVCTVTGNGLKDPDTALKDMPSVSPVPVDPVAVVEKLGL 359
           LK+I+DGWVA+GSTVVCTVTGNGLKDPDTALK MP+V PVPVDPVAVV KLGL
Sbjct: 306 LKSIEDGWVAKGSTVVCTVTGNGLKDPDTALKGMPAVIPVPVDPVAVVAKLGL 358


Lambda     K      H
   0.317    0.132    0.392 

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: 534
Number of extensions: 17
Number of successful extensions: 1
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: 360
Length of database: 359
Length adjustment: 29
Effective length of query: 331
Effective length of database: 330
Effective search space:   109230
Effective search space used:   109230
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_011781502.1 MVAN_RS21820 (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.13420.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      4e-97  311.3   0.0    4.8e-97  311.1   0.0    1.1  1  lcl|NCBI__GCF_000015305.1:WP_011781502.1  MVAN_RS21820 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011781502.1  MVAN_RS21820 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.1   0.0   4.8e-97   4.8e-97       1     340 []      15     333 ..      15     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 311.1 bits;  conditional E-value: 4.8e-97
                                 TIGR00260   1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltka 68 
                                               ++ yr  l++      ++l eg t+l+ +p+l+e  g   +++k ++++Pt++FKDrg   +++++t+a
  lcl|NCBI__GCF_000015305.1:WP_011781502.1  15 IEAYRDRLPIEdSWTTITLREGGTPLLPAPRLSEYTGC-TVHLKVEGLNPTGSFKDRG---MTMAVTEA 79 
                                               5679999999988899*********************9.*******************...******** PP

                                 TIGR00260  69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137
                                                 +g+++vlcA++G+t+a+aa a+a++a++ + vL+P+gki+   +kl++a++++ak+++i+G+FDd++
  lcl|NCBI__GCF_000015305.1:WP_011781502.1  80 VSRGQQAVLCASTGNTSASAA-AYAARAGITCAVLVPQGKIA--MGKLAQAVMHGAKIIQIDGNFDDCL 145
                                               *********************.********************..************************* PP

                                 TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205
                                               +l +++ +d +   ++ vNs+np+rie+qkt+afeiv++lg ++pd   +pv+ +gn++a++kG+ e++
  lcl|NCBI__GCF_000015305.1:WP_011781502.1 146 ELARKLTSDFP--TVSLVNSVNPFRIEGQKTAAFEIVDALG-DAPDVHSLPVGnAGNITAYWKGYTEYH 211
                                               *******7666..566689999*******************.*************************** PP

                                 TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270
                                               + g    lp ++l+ +a gaa+ v          p +d+eT++tA++ig p+++  a+e+ ++s+g + 
  lcl|NCBI__GCF_000015305.1:WP_011781502.1 212 RDGlaarLP-RMLGTQAAGAAPLVLGE-------PVSDPETIATAIRIGSPASWSSAVEAQQQSGGRFV 272
                                               *********.**********9999877.......9*********************************9 PP

                                 TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339
                                               +     +deeil a++++a+ eg+++ep++a+++a+l+k +e+g    + ++  ++vv+ +tgn+lkdp
  lcl|NCBI__GCF_000015305.1:WP_011781502.1 273 AA----TDEEILAAYHLVARAEGVFVEPASAASIAGLLKSIEDG---WVAKG--STVVCTVTGNGLKDP 332
                                               99....**************************************...99899..**************9 PP

                                 TIGR00260 340 e 340
                                               +
  lcl|NCBI__GCF_000015305.1:WP_011781502.1 333 D 333
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (359 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.95
//
[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