GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Echinicola vietnamensis KMM 6221, DSM 17526

Align candidate Echvi_0120 Echvi_0120 (3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase)
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/PF01817.21.hmm
# target sequence database:        /tmp/gapView.20990.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=75]
Accession:   PF01817.21
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    1.6e-22   66.0   0.8    3.8e-22   64.8   0.8    1.7  1  lcl|FitnessBrowser__Cola:Echvi_0120  Echvi_0120 3-deoxy-D-arabino-hep


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0120  Echvi_0120 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.8   3.8e-22   3.8e-22       1      75 []     276     354 ..     276     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.8e-22
                                          HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH...HH.S-HHHHHHHHHHHHHHH CS
                                 CM_2   1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee...ga.ldeeaierifreiisas 70 
                                          R+ Id++Dd++++LLaeR+++++++g+ K+e++l+v++ +R++ev++ +++   ++ l+e+++++++  i+++s
  lcl|FitnessBrowser__Cola:Echvi_0120 276 RSAIDHMDDQLIDLLAERFAVIDQIGAHKREHKLTVFQSDRWKEVMDSRTDkgvKKgLSEKFMKELLFSIHEES 349
                                          99*************************************************755227***************** PP

                                          HHHHH CS
                                 CM_2  71 ralqk 75 
                                          +++q+
  lcl|FitnessBrowser__Cola:Echvi_0120 350 VKRQE 354
                                          ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (75 nodes)
Target sequences:                          1  (367 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.28
//
[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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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