GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Desulfotalea psychrophila LSv54

Align candidate WP_011188872.1 DP_RS08280 (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.302739.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-184  599.9   0.0   1.2e-184  599.8   0.0    1.0  1  NCBI__GCF_000025945.1:WP_011188872.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011188872.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.8   0.0  1.2e-184  1.2e-184       1     383 [.       5     389 ..       5     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 599.8 bits;  conditional E-value: 1.2e-184
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g+fg++GG y+pe+l e+++ le+ay++a++d++f++e+ +l+++y+ rptplt+a+nlsk+ gga+iy+kre
  NCBI__GCF_000025945.1:WP_011188872.1   5 GFFGNWGGVYLPEILRETFDRLEEAYQQARNDPSFWQEYLQLMSTYSCRPTPLTYAENLSKHFGGAQIYIKRE 77 
                                           68*********************************************************************** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl+htGahk nn++gq ll+kr+Gkkr+iaetGaGqhGvatat+aa++glec++ymG+ dv+rq++nvf+me 
  NCBI__GCF_000025945.1:WP_011188872.1  78 DLNHTGAHKANNVMGQGLLVKRMGKKRVIAETGAGQHGVATATMAAKFGLECTIYMGEVDVQRQRPNVFWMEK 150
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           +ga+vvpv++Gs+tlkda+nea+rdWv++++dthyvlG+a+Gp+PfPe+v++fqs+ig+e++eqi++ +gr P
  NCBI__GCF_000025945.1:WP_011188872.1 151 MGATVVPVKDGSRTLKDAINEAFRDWVSNIDDTHYVLGTACGPAPFPEMVSWFQSIIGTEAREQIERYHGRPP 223
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGk..eGvlhGaktkllqdedGqie 290
                                             v+acvGGGsna+Gif+ f+ed+++el+gveagG G++t +haa+l+ G   +Gv +G+kt++lq++dGq++
  NCBI__GCF_000025945.1:WP_011188872.1 224 KRVYACVGGGSNAMGIFQGFLEDKKIELVGVEAGGDGLETGRHAARLAGGDasPGVAQGYKTMFLQNDDGQMR 296
                                           ************************************************996559******************* PP

                             TIGR00263 291 eahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkd 363
                                           e+hsv+aGldy+gv+P +++l e+gr+++ea+td+e+l+al+l +k+eGiipales+ha a++ k a++l+ +
  NCBI__GCF_000025945.1:WP_011188872.1 297 ETHSVAAGLDYVGVSPILSHLWEEGRVRFEAATDTEVLAALELTMKKEGIIPALESAHAFAQAFKEASDLSPE 369
                                           ************************************************************************* PP

                             TIGR00263 364 eivvvnlsGrGdkdletvak 383
                                           + +v+n+sGrGdkd++tva+
  NCBI__GCF_000025945.1:WP_011188872.1 370 DAIVINMSGRGDKDIFTVAH 389
                                           *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (410 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: 00:00:00.00
# Mc/sec: 17.36
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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