GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Magnetospirillum magneticum AMB-1

Align candidate WP_043745372.1 AMB_RS20105 (chorismate mutase)
to HMM PF01817 (CM_2)

# 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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.17614.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.5e-20   59.0   0.3    3.9e-20   58.4   0.3    1.3  1  lcl|NCBI__GCF_000009985.1:WP_043745372.1  AMB_RS20105 chorismate mutase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043745372.1  AMB_RS20105 chorismate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.3   3.9e-20   3.9e-20       1      78 [.      12      87 ..      12      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 3.9e-20
                                      CM_2  1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68
                                              R+eId+iD++l +Ll +R++l+  ia++K+++    l+p Re+++l+rl +   g     +++ av +i+r
  lcl|NCBI__GCF_000009985.1:WP_043745372.1 12 RREIDRIDDQLHDLLMRRTSLVGSIAAAKSDRR-VTLRPGREAQILRRLLArheG----AFPKLAVVRIWR 77
                                              99***************************8777.79***************5544....5*********** PP

                                      CM_2 69 eiisesralQ 78
                                              ei+ +   lQ
  lcl|NCBI__GCF_000009985.1:WP_043745372.1 78 EIVGALTGLQ 87
                                              **99887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (291 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: 9.91
//
[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