GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Pseudomonas simiae WCS417

Align candidate GFF36 PS417_00185 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta 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/TIGR00263.hmm
# target sequence database:        /tmp/gapView.14394.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00263  [M=385]
Accession:   TIGR00263
Description: trpB: tryptophan synthase, beta 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.4e-198  643.7   0.0   6.2e-198  643.5   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF36  PS417_00185 tryptophan synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF36  PS417_00185 tryptophan synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.5   0.0  6.2e-198  6.2e-198       1     384 [.      16     399 ..      16     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 643.5 bits;  conditional E-value: 6.2e-198
                         TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllh 77 
                                       g fg+fGG+yv+e+l++ + +l ++ye ak+d++fk+el ++ ++y+grp+pl+fa++l++  ggakiylkre+l+h
  lcl|FitnessBrowser__WCS417:GFF36  16 GLFGAFGGRYVAETLMPLILDLAREYEAAKEDPAFKEELAYFQRDYVGRPSPLYFAERLTEFCGGAKIYLKREELNH 92 
                                       67*************************************************************************** PP

                         TIGR00263  78 tGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpv 154
                                       tGahkinn +gq+lla+r+GkkriiaetGaG hGvatat+aa++gl+c++ymG++d+erq+ nvfrm+llga+v+pv
  lcl|FitnessBrowser__WCS417:GFF36  93 TGAHKINNCIGQILLARRMGKKRIIAETGAGMHGVATATVAARFGLQCVIYMGTTDIERQQANVFRMKLLGAEVIPV 169
                                       ***************************************************************************** PP

                         TIGR00263 155 tsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsn 231
                                         G+ tlkda+nealrdWvt+v++t+y++G+++GphP+P++vr+fq+vig+e++ q++++egrlPd ++ac+GGGsn
  lcl|FitnessBrowser__WCS417:GFF36 170 VAGTGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPYPAMVRDFQAVIGKETRDQLQAQEGRLPDSLVACIGGGSN 246
                                       ***************************************************************************** PP

                         TIGR00263 232 aiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPeh 308
                                       a+G+f++f++d++ve+igvea+G+Gi+t khaa+l+ G +GvlhG++t llqd+dGqi +ahs+saGldypg+gPeh
  lcl|FitnessBrowser__WCS417:GFF36 247 AMGLFHPFLDDQSVEIIGVEAAGHGIETGKHAASLNGGVPGVLHGNRTFLLQDDDGQIIDAHSISAGLDYPGIGPEH 323
                                       ***************************************************************************** PP

                         TIGR00263 309 aalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                       a+l+++gr++y+++td+eal+a++++++ eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd++tv+++
  lcl|FitnessBrowser__WCS417:GFF36 324 AWLHDIGRVQYTSVTDDEALDAFHKCCRLEGIIPALESAHALAEVFKRAPTLPKDHLMVVNLSGRGDKDMQTVMHH 399
                                       *************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (413 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.40
//
[ok]

This GapMind analysis is from Apr 09 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:

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. 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:

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:

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