Align candidate GFF1835 HP15_1792 (B12-dependent 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.19322.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-135 434.6 0.0 2.2e-134 433.1 0.0 1.8 2 lcl|FitnessBrowser__Marino:GFF1835 HP15_1792 B12-dependent methioni Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1835 HP15_1792 B12-dependent methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.6 0.0 0.31 0.31 40 67 .. 707 734 .. 705 744 .. 0.83 2 ! 433.1 0.0 2.2e-134 2.2e-134 1 273 [] 940 1212 .. 940 1212 .. 1.00 Alignments for each domain: == domain 1 score: -3.6 bits; conditional E-value: 0.31 Met_synt_B12 40 lfkdAqamLkkiieekllkakavvglfp 67 lf d++ +L +++++ ++ +av+ l+p lcl|FitnessBrowser__Marino:GFF1835 707 LFGDGKMFLPQVVKSARVMKQAVAHLIP 734 89999**********9999999999987 PP == domain 2 score: 433.1 bits; conditional E-value: 2.2e-134 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAnsegd 73 dl+elv+yidWtpff++W+++gkyp+i++d+k ge+a++lf+dAq++L+++i+ek+++a++v+g++pAn++gd lcl|FitnessBrowser__Marino:GFF1835 940 DLNELVDYIDWTPFFMSWDISGKYPAIFDDPKRGEAARHLFDDAQKILHRMIDEKRVSARGVIGFWPANRRGD 1012 699********************************************************************** PP Met_synt_B12 74 dievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgieelakefeaekd 146 d+++y+des +eel+tlh+Lrqq ek+ gkp ++l+Dfvap+ sg+ Dy+G+Favt+g+g+ee+ ef++++d lcl|FitnessBrowser__Marino:GFF1835 1013 DVVLYTDESCTEELTTLHHLRQQDEKAPGKPMMALSDFVAPEGSGTVDYVGGFAVTTGIGAEEFSVEFKDAND 1085 ************************************************************************* PP Met_synt_B12 147 dYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpacpdhtekktlfel 219 dY+ai+vkaladrLaeAfae++he+vr+e+Wgya+dekl n++like+Y+giRpApGYpacpdhtek+tlf+l lcl|FitnessBrowser__Marino:GFF1835 1086 DYNAIMVKALADRLAEAFAERMHERVRQEFWGYAADEKLANDDLIKERYRGIRPAPGYPACPDHTEKATLFSL 1158 ************************************************************************* PP Met_synt_B12 220 ldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 l+a++++gieLte++am P+a+vsG+yfahpe++yFavgki+ dqvedya+rkg lcl|FitnessBrowser__Marino:GFF1835 1159 LEATDTAGIELTEHFAMFPTAAVSGWYFAHPESKYFAVGKIGADQVEDYAERKG 1212 ****************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1232 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: 18.64 // [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