GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Enterococcus termitis LMG 8895

Align candidate WP_069662459.1 BCR25_RS04685 (chorismate mutase)
to HMM TIGR01805 (chorismate mutase (EC 5.4.99.5))

# 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/TIGR01805.hmm
# target sequence database:        /tmp/gapView.1955740.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01805  [M=81]
Accession:   TIGR01805
Description: CM_mono_grmpos: chorismate mutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.1e-33   98.7   4.6    1.7e-32   97.8   4.6    1.4  1  NCBI__GCF_001730305.1:WP_069662459.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069662459.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   4.6   1.7e-32   1.7e-32       1      81 []     194     274 ..     194     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.7e-32
                             TIGR01805   1 LeliRkkideiDdklvkLleeRlelvkevaalKkkngievfDskREqkvldkvlkrvenkeYeetleeffsnl 73 
                                           L  +R+ki+e+D+k+v LleeR++ v  +aa+Kk + +e++D+ REq+vl k+ ++v n+eY+e+l+e+++++
  NCBI__GCF_001730305.1:WP_069662459.1 194 LTSQREKINELDKKIVALLEERMDAVSSIAAIKKTSDKEILDTAREQEVLAKIDSYVVNAEYKEVLKETYQGI 266
                                           5679********************************************************************* PP

                             TIGR01805  74 ldlSkelq 81 
                                           +d+Sk++q
  NCBI__GCF_001730305.1:WP_069662459.1 267 MDASKHFQ 274
                                           ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (81 nodes)
Target sequences:                          1  (279 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.14
//
[ok]

This GapMind analysis is from Jul 26 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