GapMind for Amino acid biosynthesis

 

Alignments for a candidate for B12-reactivation-domain in Phyllobacterium endophyticum PEPV15

Align candidate WP_106717619.1 CU100_RS16195 (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.2153415.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-129  416.2   0.0   4.9e-129  415.6   0.0    1.3  1  NCBI__GCF_003010935.1:WP_106717619.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106717619.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.6   0.0  4.9e-129  4.9e-129       1     273 []     960    1232 ..     960    1232 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.6 bits;  conditional E-value: 4.9e-129
                          Met_synt_B12    1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAnse 71  
                                            dl+e+++yidWtpffq+Welkg+yp+il+d+k+ge+a++lf+dAqamLkkii+ek+++ kavvgl+pA ++
  NCBI__GCF_003010935.1:WP_106717619.1  960 DLAEIARYIDWTPFFQTWELKGRYPAILDDDKQGEAARQLFDDAQAMLKKIIAEKWFNPKAVVGLWPAGTV 1030
                                            699******************************************************************** PP

                          Met_synt_B12   72 gddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgieelakefe 142 
                                            gddi v+ade+rseelat++tLrqq +k++g+pn++l+Df+ap++s vkDy+G+F+vtag++  ++a++fe
  NCBI__GCF_003010935.1:WP_106717619.1 1031 GDDIRVFADERRSEELATFYTLRQQLSKRDGRPNVALSDFIAPEDSAVKDYMGAFVVTAGIEEIAIAERFE 1101
                                            *********************************************************************** PP

                          Met_synt_B12  143 aekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpacpdhtek 213 
                                            +++ddYs+ilvkaladr+aeAfael+he+vrke+W ya+de+ls eeli e Y+giRpApGYpa+pdhtek
  NCBI__GCF_003010935.1:WP_106717619.1 1102 RANDDYSSILVKALADRFAEAFAELMHERVRKEFWSYAPDENLSPEELIGEPYRGIRPAPGYPAQPDHTEK 1172
                                            *********************************************************************** PP

                          Met_synt_B12  214 ktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 
                                            +tlf++ldae++i+++Ltes+am+P +svsG+y+ hpe+ yF+v+k+e+dqvedy  rk+
  NCBI__GCF_003010935.1:WP_106717619.1 1173 ATLFRILDAEAQINVRLTESFAMWPGSSVSGIYIGHPESYYFGVAKVERDQVEDYSVRKQ 1232
                                            *********************************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (273 nodes)
Target sequences:                          1  (1258 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: 46.20
//
[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