Align candidate WP_084275467.1 B8779_RS05105 (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.8671.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-35 108.8 0.0 3.1e-35 108.0 0.0 1.4 1 lcl|NCBI__GCF_900176045.1:WP_084275467.1 B8779_RS05105 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084275467.1 B8779_RS05105 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 108.0 0.0 3.1e-35 3.1e-35 54 257 .. 939 1148 .] 894 1148 .] 0.80 Alignments for each domain: == domain 1 score: 108.0 bits; conditional E-value: 3.1e-35 Met_synt_B12 54 ekllkakavvglfpAnsegddievy.......adesrse........elatlhtLrqqaekeegkpn 105 ++ ++ ++g +pA+++++++ v+ +de+ ++ + ++ t +q ++ p+ lcl|NCBI__GCF_900176045.1:WP_084275467.1 939 KDIFQPVILYGYWPARAVDNELYVFgeefgwqRDEDANRepieniigDAIEIFTFPRQ----SKPPH 1001 3457888899999999999999999666666522222222333333323333333333....45799 PP Met_synt_B12 106 lclaDfvapkesgvkDyiGlFavtaglgieelakefeaekddYsailvkaladrLaeAfaellhekv 172 +c+aD+ + ++ D+ ++ +v+ag + +e+ e+ ++ + lv+ l+ LaeA+ae h+++ lcl|NCBI__GCF_900176045.1:WP_084275467.1 1002 RCIADYFHA---DRMDVSAFTCVSAGSKFSEYEGELFKAGKYHEYHLVHGLSVELAEALAEIAHKQI 1065 *******99...467999999************9999998888888********************* PP Met_synt_B12 173 rkelWgyakdeklsneelikekYqgiRpApGYpacpdhtekktlfelldaeekigieLteslamtPa 239 r e g ++ek + +++ Yqg R++pGYpacpd + ++++f+ll+ ee gieL+e++ ++P+ lcl|NCBI__GCF_900176045.1:WP_084275467.1 1066 RIE-LGILRNEKADLRDVKMVGYQGARYSPGYPACPDLELNRHIFNLLKPEE-FGIELSETFQIHPE 1130 **9.6999********************************************.************** PP Met_synt_B12 240 asvsGlyfahpearyFav 257 +s +++++ hpea+yF+v lcl|NCBI__GCF_900176045.1:WP_084275467.1 1131 QSTCAIVVHHPEAKYFNV 1148 ****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1148 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: 18.91 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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