GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpA in Desulfovibrio vulgaris Miyazaki F

Align candidate 8501003 DvMF_1740 (tryptophan synthase subunit alpha (RefSeq))
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))

# 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/TIGR00262.hmm
# target sequence database:        /tmp/gapView.29562.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00262  [M=256]
Accession:   TIGR00262
Description: trpA: tryptophan synthase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.1e-66  210.3   0.0    1.3e-66  210.1   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501003  DvMF_1740 tryptophan synthase su


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501003  DvMF_1740 tryptophan synthase subunit alpha (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.0   1.3e-66   1.3e-66       6     246 ..      30     267 ..      25     270 .] 0.95

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 1.3e-66
                         TIGR00262   6 kkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkvr 82 
                                       +++  a+vpF+tag P+l++  e ++ l + Gad++E+GvpfsDP+aDGp++ aa+lRAl++gv+++ +l+ lk+ r
  lcl|FitnessBrowser__Miya:8501003  30 AAGRPALVPFLTAGFPTLDRFWEEMDGLDRGGADVIEIGVPFSDPVADGPVVEAASLRALENGVTLRWILDGLKA-R 105
                                       566779**************************************************************9997765.6 PP

                         TIGR00262  83 ekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkki 159
                                       + + ++ +vl+ yyn+ +++g+e+  a a++agv g +v+DlPlee ++++   + +g++ i lv P+++eer+ + 
  lcl|FitnessBrowser__Miya:8501003 106 AGRYEAELVLMGYYNPFLQYGLENLAADAAAAGVAGFIVPDLPLEEDAEMRALLAARGIDLIALVGPNTSEERMAEY 182
                                       66699************************************************************************ PP

                         TIGR00262 160 aekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiiee 236
                                       a  ++G+vY+vsv+G+tg+re +  ev + ++++++  + P ++GFGi ++ q++   +   d+v+ GsAl++ i+ 
  lcl|FitnessBrowser__Miya:8501003 183 AAVASGYVYVVSVLGITGVREGLPPEVPQTLARARKAFRLPLALGFGIKEPKQLEGFPDR-PDAVVFGSALLRHIDA 258
                                       ***********************************************************9.788***********99 PP

                         TIGR00262 237 klddeekale 246
                                         +  e +l+
  lcl|FitnessBrowser__Miya:8501003 259 G-NSAESFLA 267
                                       8.66777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (270 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: 6.06
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, or view the source code, or see 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