Align candidate WP_086511312.1 BZY95_RS18210 (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.16400.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-128 412.3 0.1 7.4e-128 411.8 0.1 1.3 1 lcl|NCBI__GCF_002151265.1:WP_086511312.1 BZY95_RS18210 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511312.1 BZY95_RS18210 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.8 0.1 7.4e-128 7.4e-128 1 273 [] 941 1220 .. 941 1220 .. 0.98 Alignments for each domain: == domain 1 score: 411.8 bits; conditional E-value: 7.4e-128 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 d+eelve idWtpff++Wel+gkypki++d +vge+a++lf+dAq+mL+k+i+ k+++a++v+gl+p lcl|NCBI__GCF_002151265.1:WP_086511312.1 941 DIEELVERIDWTPFFMSWELAGKYPKIFDDAVVGEAARNLFADAQQMLRKLIDGKHVEARGVIGLWP 1007 699**************************************************************** PP Met_synt_B12 68 Ansegdd.ievyadesrseelatlhtLrqqaekeegkpnlclaDfvapk......esgvkDyiGlFa 127 Ans++dd ievyadesrse++a+lh++rqq++k+++ +++laDfvap+ e+++ D++G+Fa lcl|NCBI__GCF_002151265.1:WP_086511312.1 1008 ANSVDDDvIEVYADESRSEVIARLHHIRQQTTKNRDGVCYSLADFVAPRydadgnERDQLDWVGGFA 1074 ****988799**************************************8777766777889****** PP Met_synt_B12 128 vtaglgieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikek 194 vt+g+g+e+la++++a+ ddYsai+v+al+drLaeAfae++he+vrke+Wgy +de+l+n++li+ek lcl|NCBI__GCF_002151265.1:WP_086511312.1 1075 VTTGHGVEALAERYKAAGDDYSAIMVQALTDRLAEAFAERMHERVRKEFWGYVPDETLDNDALIAEK 1141 ******************************************************************* PP Met_synt_B12 195 YqgiRpApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkie 261 YqgiRpApGYpacpdhtek+tlf+llda+e++gieLte++am+Paa+vsG+yf+hp+a+yF+ gki+ lcl|NCBI__GCF_002151265.1:WP_086511312.1 1142 YQGIRPAPGYPACPDHTEKRTLFQLLDATENAGIELTENFAMWPAAAVSGWYFSHPQAKYFSTGKIT 1208 ******************************************************************* PP Met_synt_B12 262 kdqvedyakrkg 273 +dqve a+rkg lcl|NCBI__GCF_002151265.1:WP_086511312.1 1209 RDQVEALAQRKG 1220 **********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1239 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 21.25 // [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