Align candidate WP_020562591.1 A3OW_RS0106365 (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.4637.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-138 446.3 0.0 3.8e-138 445.5 0.0 1.4 1 lcl|NCBI__GCF_000372865.1:WP_020562591.1 A3OW_RS0106365 methionine syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_020562591.1 A3OW_RS0106365 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.5 0.0 3.8e-138 3.8e-138 2 273 .] 937 1208 .. 936 1208 .. 0.99 Alignments for each domain: == domain 1 score: 445.5 bits; conditional E-value: 3.8e-138 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpA 68 le+lv yidW+pff++Wel+g+ypkil+d+ vg+ea+klf+dAq mLkkii+e++l+a+av+g+fpA lcl|NCBI__GCF_000372865.1:WP_020562591.1 937 LETLVWYIDWSPFFHTWELAGRYPKILDDPLVGTEARKLFDDAQVMLKKIISEQWLTARAVIGFFPA 1003 899**************************************************************** PP Met_synt_B12 69 nsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgie 135 nsegdd+++y+desr+e+ + l++Lrqq+ k+ g+pn+cl+Df+ap+ sg++Dy+G+Favt+g+gie lcl|NCBI__GCF_000372865.1:WP_020562591.1 1004 NSEGDDVILYTDESRTEQREILRHLRQQNVKAPGRPNYCLSDFIAPAGSGIADYLGAFAVTTGIGIE 1070 ******************************************************************* PP Met_synt_B12 136 elakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpAp 202 ++++efe+e+ddYsai++kaladrLaeAfae++h+ vrk++Wgya+de+ +ne+li+e+YqgiRpAp lcl|NCBI__GCF_000372865.1:WP_020562591.1 1071 QKLREFEREHDDYSAIMLKALADRLAEAFAEYMHQAVRKDHWGYARDENYDNEQLINETYQGIRPAP 1137 ******************************************************************* PP Met_synt_B12 203 GYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedya 269 GYpacpdhtek++lfell+++e++gieLtes+am+Pa++vsG+yfahpe++yF+vgki+kdq++dya lcl|NCBI__GCF_000372865.1:WP_020562591.1 1138 GYPACPDHTEKAKLFELLNVTENTGIELTESYAMYPASAVSGWYFAHPESQYFNVGKINKDQLQDYA 1204 ******************************************************************* PP Met_synt_B12 270 krkg 273 +rkg lcl|NCBI__GCF_000372865.1:WP_020562591.1 1205 RRKG 1208 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1224 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: 00:00:00.01 # Mc/sec: 33.25 // [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