GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Pseudomonas fluorescens FW300-N1B4

Align candidate Pf1N1B4_1831 (Tryptophan synthase beta chain (EC 4.2.1.20))
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.11305.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.8e-198  644.2   0.0   4.4e-198  644.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831  Tryptophan synthase beta chain (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831  Tryptophan synthase beta chain (EC 4.2.1.20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.0   0.0  4.4e-198  4.4e-198       1     384 [.      14     397 ..      14     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 644.0 bits;  conditional E-value: 4.4e-198
                                      TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklg 64 
                                                    g fg+fGG+yv+e+l++ + +l ++ye ak+d++fk+el ++ ++y+grp+pl+fa++l++  g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831  14 GLFGAFGGRYVAETLMPLILDLAREYEAAKEDPAFKEELAYFQRDYVGRPSPLYFAERLTEFCG 77 
                                                    67************************************************************** PP

                                      TIGR00263  65 gakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevy 128
                                                    gakiylkre+l+htGahkinn +gq+lla+r+GkkriiaetGaG hGvatat+aa++gl+c++y
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831  78 GAKIYLKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGMHGVATATVAARFGLDCVIY 141
                                                    **************************************************************** PP

                                      TIGR00263 129 mGaedverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPf 192
                                                    mG++d+erq+ nvfrm+llga+v+pv  G+ tlkda+nealrdWvt+v++t+y++G+++GphP+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 142 MGTTDIERQQANVFRMKLLGAEVIPVVAGTGTLKDAMNEALRDWVTNVDSTFYLIGTVAGPHPY 205
                                                    **************************************************************** PP

                                      TIGR00263 193 PeivrefqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkG 256
                                                    P++vr+fq+vig+e++eq++++egrlPd ++ac+GGGsna+G+f++f++d++ve+igvea+G G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 206 PAMVRDFQAVIGKETREQLQAQEGRLPDSLVACIGGGSNAMGLFHPFLDDKSVEIIGVEAAGYG 269
                                                    **************************************************************** PP

                                      TIGR00263 257 idtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeye 320
                                                    i+t khaa+l+ G +GvlhG++t llqdedGqi +ahs+saGldypg+gPeha+l+++gr++y+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 270 IETGKHAASLNGGVPGVLHGNRTFLLQDEDGQIIDAHSISAGLDYPGIGPEHAWLHDIGRVQYT 333
                                                    **************************************************************** PP

                                      TIGR00263 321 aitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384
                                                    ++td+eal+a++++++ eGiipales+hala + k ap+l+kd+++vvnlsGrGdkd++tv+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1831 334 SVTDDEALDAFHKCCRLEGIIPALESAHALAEVFKRAPTLPKDHLMVVNLSGRGDKDMQTVMHH 397
                                                    *************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (409 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: 11.48
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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