GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Dyella japonica UNC79MFTsu3.2

Align candidate N515DRAFT_0115 N515DRAFT_0115 (tryptophan synthase beta chain)
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.8725.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.3e-193  626.8   0.7   8.3e-193  626.6   0.7    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115  N515DRAFT_0115 tryptophan syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0115  N515DRAFT_0115 tryptophan synthase beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.6   0.7  8.3e-193  8.3e-193       1     383 [.      13     395 ..      13     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: 626.6 bits;  conditional E-value: 8.3e-193
                                    TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklgga 66 
                                                  g+fg+fGGqyv+e+l++ ++el++ay ++++d+ef +el++ lk y+grp+p+++a+ ls+++gga
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115  13 GRFGDFGGQYVAETLMAPIAELTEAYLRLREDPEFLAELDRDLKYYVGRPSPIYHAEGLSRHVGGA 78 
                                                  78**************************************************************** PP

                                    TIGR00263  67 kiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGae 132
                                                  +i lkredl+htGahkinn++gqal+akr+Gk r+iaetGaGqhGva+at+aa++gl+c+vymGa 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115  79 QILLKREDLNHTGAHKINNTIGQALVAKRMGKPRVIAETGAGQHGVASATVAARFGLKCVVYMGAV 144
                                                  ****************************************************************** PP

                                    TIGR00263 133 dverqklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivre 198
                                                  d+erqk+nv+rm+llga+vvpvtsGsktlkda+nea+rdWvt+v+dt+y++G+++GphP+P +vr+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 145 DIERQKINVYRMKLLGAEVVPVTSGSKTLKDALNEAMRDWVTNVADTFYIIGTVAGPHPYPMMVRD 210
                                                  ****************************************************************** PP

                                    TIGR00263 199 fqsvigeevkeqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaa 264
                                                  f +++g+e++eq+le+ grlPda+ acvGGGsnaiG+f+af++d +v+++g ea+G+Gi+t +haa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 211 FNAIVGREAREQMLEQYGRLPDAITACVGGGSNAIGLFHAFLNDANVRIVGAEAAGEGIATGHHAA 276
                                                  ****************************************************************** PP

                                    TIGR00263 265 tlskGkeGvlhGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealea 330
                                                  +l++G++GvlhG++t++l d++Gqi+e+hsvsaGldypgvgPeha+l++ graey+ itd+ealea
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 277 SLAAGRPGVLHGNRTYVLCDDNGQITETHSVSAGLDYPGVGPEHAFLKDAGRAEYVGITDDEALEA 342
                                                  ****************************************************************** PP

                                    TIGR00263 331 lkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrGdkdletvak 383
                                                  ++ll+++eGi++alessha+a+++kla +++kd++v++nlsGrGdkd++t+a 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0115 343 FHLLARTEGILAALESSHAVAQAIKLAREMPKDQLVLCNLSGRGDKDVHTIAA 395
                                                  **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 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: 9.01
//
[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