Alignments for a candidate for trpA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpA in Pseudomonas putida KT2440

Align candidate PP_0082 PP_0082 (tryptophan synthase alpha chain)
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.30437.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-86  275.9   0.0    1.2e-86  275.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0082  PP_0082 tryptophan synthase alph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0082  PP_0082 tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.7   0.0   1.2e-86   1.2e-86       1     252 [.       8     257 ..       8     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: 275.7 bits;  conditional E-value: 1.2e-86
                           TIGR00262   1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekal 75 
                                         f++lk+++  a+v+FvtagdP ++ sl+i+k l  aGad++ElG+pf DP+aDG +iq a+lRAl+ag ++ k+l
  lcl|FitnessBrowser__Putida:PP_0082   8 FAELKAEGRSALVTFVTAGDPGYDASLQILKGLPAAGADVIELGMPFTDPMADGVAIQLATLRALEAGQTLVKTL 82 
                                         7899*********************************************************************** PP

                           TIGR00262  76 ellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPt 150
                                         ++++++r ++++ Pivl+ yyn+i++ gv++F+++akeagvdg++++DlP e  ++l   a+  g++ i l +Pt
  lcl|FitnessBrowser__Putida:PP_0082  83 QMVREFRVDNQTTPIVLMGYYNPIHRFGVDTFVTQAKEAGVDGLIIVDLPPEHDAELATPAQAAGIDFIRLTTPT 157
                                         *************************************************************************** PP

                           TIGR00262 151 aeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvi 225
                                         +++ rl ++ e+s+GfvY vsvaGvtga +  +e+v+e+i++++++++ P+ vGFGi  +eq+ ++  l adgv+
  lcl|FitnessBrowser__Putida:PP_0082 158 TDDARLPRVLERSSGFVYYVSVAGVTGAGSATTEHVTEAIARLRRHTDLPISVGFGIRTPEQAANIARL-ADGVV 231
                                         *********************************************************************.99*** PP

                           TIGR00262 226 vGsAlvkiieeklddeekaleeleefv 252
                                         vGsAlv++i++ +   ++a+ ++ +++
  lcl|FitnessBrowser__Putida:PP_0082 232 VGSALVDKIAQAKS-ADQAVTDVLSLC 257
                                         ***********965.666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (256 nodes)
Target sequences:                          1  (269 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: 00:00:00.00
# Mc/sec: 9.01
//
[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 (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, 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

GapMind for Amino acid biosynthesis