GapMind for Amino acid biosynthesis

 

Alignments for a candidate for B12-reactivation-domain in Magnetospirillum magneticum AMB-1

Align candidate WP_043743213.1 AMB_RS02225 (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.24147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.4e-52  164.1   0.0    3.4e-52  163.6   0.0    1.2  1  lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   0.0   3.4e-52   3.4e-52       2     257 ..     911    1157 .]     910    1157 .] 0.92

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 3.4e-52
                              Met_synt_B12    2 leelveyidWtpffqa.WelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67  
                                                l++l+++++ t+ +q+ W+ +++ ++i e   ++ + k++   A +mLk+  +e+ l+ +av+g ++
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  911 LQNLIPFLNETMLYQFhWGYRKQGKSIEE--FKAWAHKEIRPVAMDMLKRCAKEEILRPQAVYGYWK 975 
                                                78899999999988854888888777755..55778899999************************* PP

                              Met_synt_B12   68 AnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 
                                                A s++d ++++a++  ++e+a++++ rq +     +  lc+aDf +p ++ v+D+iGl +vt+g  +
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  976 AASDNDSVVLFAEDG-TTEVARFPFPRQAK-----DGGLCIADFFRPVSDPVRDVIGLQVVTMGKRA 1036
                                                **********97666.55689******993.....458***************************** PP

                              Met_synt_B12  135 eelakefeaekddYsa.ilvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRp 200 
                                                 e+a+++ ++ d+Y++ + ++ l+  +aeA+ae++h+++r e  g+a++++ ++++l+k++Y+g R 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1037 TEVAQDWFKA-DKYQDyLYLHGLSVEMAEAMAEYVHKRIRSE-LGFAAEDAADMDRLLKQNYRGSRF 1101
                                                *******999.99987256899*******************9.6*********************** PP

                              Met_synt_B12  201 ApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFav 257 
                                                ++GYpacp  + +++l +ll ae+ ig++L+e++ + P++s s+++  hp+a+yF+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1102 SFGYPACPRIEDQTQLLSLLGAER-IGVTLSEEFQLEPEQSTSAIVTVHPQAKYFSV 1157
                                                ***********************9.******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (273 nodes)
Target sequences:                          1  (1157 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: 00:00:00.01
# Mc/sec: 20.88
//
[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