Align candidate WP_028489777.1 Q394_RS0113740 (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.1728.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-133 429.4 0.0 4.7e-133 428.8 0.0 1.3 1 lcl|NCBI__GCF_000621325.1:WP_028489777.1 Q394_RS0113740 methionine syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028489777.1 Q394_RS0113740 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.8 0.0 4.7e-133 4.7e-133 2 273 .] 938 1209 .. 937 1209 .. 0.99 Alignments for each domain: == domain 1 score: 428.8 bits; conditional E-value: 4.7e-133 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpA 68 l+el+e idWtpff++We++g++p+il+de vgee +kl++dAqamLk++++ek+++aka+vg+fpA lcl|NCBI__GCF_000621325.1:WP_028489777.1 938 LAELMERIDWTPFFRSWEMAGRFPDILTDEIVGEECTKLYADAQAMLKTLVDEKWVQAKAIVGFFPA 1004 89***************************************************************** PP Met_synt_B12 69 nsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgie 135 n++gdd+++y+desrse+l++lh Lr q+e++ ++pn+cl Dfvap esg++D++G+Fav++g+gie lcl|NCBI__GCF_000621325.1:WP_028489777.1 1005 NAQGDDVVLYTDESRSEQLTVLHNLRMQMERNGQQPNFCLGDFVAPIESGKADWMGVFAVSTGFGIE 1071 ******************************************************************* PP Met_synt_B12 136 elakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpAp 202 ++k+f+a++ddYsai+++al+drLaeA+ae++he+vrke+Wgya+de+l+n+++i+ekYqgiRpAp lcl|NCBI__GCF_000621325.1:WP_028489777.1 1072 PHLKAFRAKHDDYSAIMLEALCDRLAEALAERMHERVRKEFWGYAADETLDNNAMIAEKYQGIRPAP 1138 ******************************************************************* PP Met_synt_B12 203 GYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedya 269 GYpacpdhtek+tl++lld+e+++g+eLt s+am+Pa+svsG+yf+hpe+ryF++g+i++dqv+dya lcl|NCBI__GCF_000621325.1:WP_028489777.1 1139 GYPACPDHTEKATLWTLLDVEANTGMELTSSFAMYPASSVSGWYFSHPESRYFGIGRIARDQVDDYA 1205 ******************************************************************* PP Met_synt_B12 270 krkg 273 krkg lcl|NCBI__GCF_000621325.1:WP_028489777.1 1206 KRKG 1209 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1227 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: 34.01 // [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