GapMind for Amino acid biosynthesis

 

Alignments for a candidate for B12-reactivation-domain in Pseudomonas fluorescens FW300-N1B4

Align candidate Pf1N1B4_5661 (5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13))
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.28653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   7.1e-127  408.5   0.1   1.1e-126  407.9   0.1    1.3  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  5-methyltetrahydrofolate--homocy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   0.1  1.1e-126  1.1e-126       1     273 []     941    1218 ..     941    1218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 1.1e-126
                                   Met_synt_B12    1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakav 62  
                                                     dl+ l+eyidWtpff +W+l+gk+p+il+de+vge+a++l++dAq+mL+k+i+ekl++a+av
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661  941 DLKVLAEYIDWTPFFISWDLAGKFPRILKDEVVGEAATALYADAQEMLAKLIDEKLISARAV 1002
                                                     58899********************************************************* PP

                                   Met_synt_B12   63 vglfpAnse.gddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyi 123 
                                                     +g++pAn++ +ddievy+d+   + la+lh+Lrqq  k++gkpn++laDfvapk+sgv+Dy+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1003 FGFWPANQVrDDDIEVYDDDG--KPLAKLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYV 1062
                                                     ********95689***96666..689************************************ PP

                                   Met_synt_B12  124 GlFavtaglgieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdekl 185 
                                                     G+F++tag+g+ee+ak+++++ ddY++i+vkaladrLaeA+ae+lh++vrk++Wgyakde+l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1063 GGFITTAGIGAEEVAKAYQDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYAKDETL 1124
                                                     ************************************************************** PP

                                   Met_synt_B12  186 sneelikekYqgiRpApGYpacpdhtekktlfelldaeek......igieLteslamtPaas 241 
                                                     +ne+like+Y+giRpApGYpacpdhtek+tlf+lld e++       g+ Lte++am Paa+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1125 DNEALIKEQYTGIRPAPGYPACPDHTEKATLFKLLDPEAEelkagrSGVFLTEHYAMFPAAA 1186
                                                     ***********************************988643333338*************** PP

                                   Met_synt_B12  242 vsGlyfahpearyFavgkiekdqvedyakrkg 273 
                                                     vsG+yfahp+a+yFavgki+kdqv++y++rkg
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1187 VSGWYFAHPQAQYFAVGKIDKDQVQSYTSRKG 1218
                                                     ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (273 nodes)
Target sequences:                          1  (1236 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 18.22
//
[ok]

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

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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