GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpB in Desulfovibrio vulgaris Miyazaki F

Align candidate 8501513 DvMF_2237 (tryptophan synthase subunit beta (RefSeq))
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.18274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.2e-185  600.9   0.1   6.1e-185  600.7   0.1    1.0  1  lcl|FitnessBrowser__Miya:8501513  DvMF_2237 tryptophan synthase su


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501513  DvMF_2237 tryptophan synthase subunit beta (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.7   0.1  6.1e-185  6.1e-185       1     383 [.      46     428 ..      46     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 600.7 bits;  conditional E-value: 6.1e-185
                         TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredllh 77 
                                       g fg +GGqyvpe + + l+el +++e++++d++f +ele++l +y+gr+tpl+ ++nl+ +lggakiylkredl+h
  lcl|FitnessBrowser__Miya:8501513  46 GLFGPYGGQYVPEHIKPVLDELAATFERYHADPDFLAELEYYLTRYSGRQTPLFLCANLTARLGGAKIYLKREDLNH 122
                                       67*************************************************************************** PP

                         TIGR00263  78 tGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgakvvpv 154
                                        Gahk+nn++gq+llakr+Gkk++iaetGaGqhGvata+ aal+g++c+++mGaed+erqklnvfrm+++ga+vvp 
  lcl|FitnessBrowser__Miya:8501513 123 LGAHKVNNTIGQILLAKRMGKKKVIAETGAGQHGVATAATAALMGMQCTIHMGAEDMERQKLNVFRMRMMGAEVVPA 199
                                       ***************************************************************************** PP

                         TIGR00263 155 tsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviacvGGGsn 231
                                        sG++tlk+av+eal +W ++ e+t+y+lGsavGphP+P+ivr+fqsvig+e+++q+le+egrlPd  +acvGGGsn
  lcl|FitnessBrowser__Miya:8501513 200 MSGQRTLKEAVDEALAAWLGDAENTFYLLGSAVGPHPYPRIVRHFQSVIGREARAQMLEAEGRLPDCAVACVGGGSN 276
                                       ***************************************************************************** PP

                         TIGR00263 232 aiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPeh 308
                                       aiG+fa+fi de v+ligve++G+G+   +haatl  G++Gv+hG+++++l+de G+   ++s+saGldypgvgPeh
  lcl|FitnessBrowser__Miya:8501513 277 AIGLFAEFIADEGVRLIGVEPAGRGLTYGDHAATLCMGTPGVMHGFHSYMLKDEAGEPAAVYSISAGLDYPGVGPEH 353
                                       ***************************************************************************** PP

                         TIGR00263 309 aalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                       ++l+++graey ++td+eal+a+  ls++eGiipalesshala+++klap+l +d+i++vnlsGrGdkd+++v +
  lcl|FitnessBrowser__Miya:8501513 354 SHLKDIGRAEYASVTDAEALDAFFILSRTEGIIPALESSHALAHAMKLAPALGRDAIILVNLSGRGDKDVAQVEE 428
                                       ***********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (440 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: 11.80
//
[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