Alignments for a candidate for B12-reactivation-domain in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for B12-reactivation-domain in Burkholderia phytofirmans PsJN

Align candidate BPHYT_RS02305 BPHYT_RS02305 (methionine synthase)
to HMM PF02965 (Met_synt_B12)

# 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/PF02965.21.hmm
# target sequence database:        /tmp/gapView.2548.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Met_synt_B12  [M=273]
Accession:   PF02965.21
Description: Vitamin B12 dependent methionine synthase, activation domain
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-124  401.4   0.0   3.2e-124  399.8   0.0    1.9  2  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  BPHYT_RS02305 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS02305  BPHYT_RS02305 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.14      0.14     103     126 ..     452     475 ..     370     519 .. 0.53
   2 !  399.8   0.0  3.2e-124  3.2e-124       1     271 [.     612     886 ..     612     888 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.14
                             Met_synt_B12 103 kpnlclaDfvapkesgvkDyiGlF 126
                                                 ++  D +a+++ + +D iGl 
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305 452 GVMVSCNDILAKAKVEGADIIGLS 475
                                              334455555555555555666554 PP

  == domain 2  score: 399.8 bits;  conditional E-value: 3.2e-124
                             Met_synt_B12   1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAns 70 
                                              dl+el++yidW pffq+W+l+g yp+il+de vge+a+++f+d+++mL+++i+ ++l+a++v++l+pAn+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305 612 DLSELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSMLARLIQGRWLQANGVIALLPANT 681
                                              699******************************************************************* PP

                             Met_synt_B12  71 eg.ddievyadesrseelatlhtLrqqaeke....egkpnlclaDfvapkesgvkDyiGlFavtaglgie 135
                                              ++ ddie+y+desrse++ t++ Lrqq+ ++      +pn++laDf+apk+sgv+DyiG+Favtaglg++
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305 682 VNdDDIEIYTDESRSEVALTWRNLRQQSVRPvvdgVMRPNRSLADFIAPKDSGVADYIGMFAVTAGLGVD 751
                                              96388**********************99988877889******************************** PP

                             Met_synt_B12 136 elakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYp 205
                                               + k+fe+++ddYsai++kaladr+aeAfae lh++vr++lWgya+ e+lsn++li+ekY+giRpApGYp
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305 752 VKEKQFEKDHDDYSAIMLKALADRFAEAFAEALHARVRRDLWGYANAETLSNDDLIAEKYHGIRPAPGYP 821
                                              ********************************************************************** PP

                             Met_synt_B12 206 acpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakr 271
                                              acpdh  k+++f++l+a+e ig+++teslam PaasvsG+y+ahp+++yF+vgki++dq+edyakr
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305 822 ACPDHLVKRDMFDVLHATE-IGMSVTESLAMLPAASVSGFYLAHPDSTYFSVGKIGQDQLEDYAKR 886
                                              *******************.*********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (273 nodes)
Target sequences:                          1  (902 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: 25.17
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis