Align candidate AO356_00545 AO356_00545 (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.19413.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-125 403.8 0.0 3.3e-125 403.1 0.0 1.4 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 AO356_00545 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 AO356_00545 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.1 0.0 3.3e-125 3.3e-125 1 273 [] 941 1218 .. 941 1218 .. 0.96 Alignments for each domain: == domain 1 score: 403.1 bits; conditional E-value: 3.3e-125 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkaka 61 dl+ l+eyidWtpff +W+l+gkyp+il+de+vge+a++l++dA+amL+k+i+ekl++a+a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 941 DLNVLAEYIDWTPFFISWDLAGKYPRILTDEVVGEAATALYADARAMLRKLIDEKLISARA 1001 58899******************************************************** PP Met_synt_B12 62 vvglfpAnse.gddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkD 121 v+g++pAn++ +dd+evy d+ + la+lh+Lrqq k++gkpn++laDfvapk+sgv+D lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 1002 VFGFWPANQVhDDDLEVYGDDG--KPLARLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTD 1060 *********94588****8877..689********************************** PP Met_synt_B12 122 yiGlFavtaglgieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakd 182 y+G+F++tag+g+ee+ak+++++ ddY++i+vkaladrLaeA+ae+lh++vrke+Wgya+d lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 1061 YVGGFITTAGIGAEEVAKAYQEAGDDYNSIMVKALADRLAEACAEWLHQQVRKEHWGYARD 1121 ************************************************************* PP Met_synt_B12 183 eklsneelikekYqgiRpApGYpacpdhtekktlfelldaee......kigieLteslamt 237 e+l+ne+like+Y+giRpApGYpacpdhtek+tlf+lld e+ + g+ Lte++am lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 1122 ESLDNEALIKEQYTGIRPAPGYPACPDHTEKATLFRLLDPEAselkagRSGVFLTEHYAMF 1182 **************************************9986333333589********** PP Met_synt_B12 238 PaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 Paa+vsG+yfahp+a+yFavgki+kdqv++y++rkg lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00545 1183 PAAAVSGWYFAHPQAQYFAVGKIDKDQVQSYTARKG 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 24.19 // [ok]
This GapMind analysis is from Apr 09 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