Align candidate 200213 SO1030 (5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file))
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.25395.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-133 427.8 0.0 1.5e-132 427.2 0.0 1.3 1 lcl|FitnessBrowser__MR1:200213 SO1030 5-methyltetrahydrofolate- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200213 SO1030 5-methyltetrahydrofolate--homocysteine methyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.2 0.0 1.5e-132 1.5e-132 2 273 .] 954 1225 .. 953 1225 .. 0.99 Alignments for each domain: == domain 1 score: 427.2 bits; conditional E-value: 1.5e-132 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAnseg.ddiev 77 l++lv+ idWtpff+aWel+g+yp+il+d++vg ea+klf+d++amLkkiieek+l+ak+v+glfpAn++g ddie+ lcl|FitnessBrowser__MR1:200213 954 LTDLVDRIDWTPFFRAWELHGHYPEILSDKVVGVEAQKLFSDGKAMLKKIIEEKWLTAKGVIGLFPANTVGfDDIEL 1030 899*******************************************************************99***** PP Met_synt_B12 78 yadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgieelakefeaekddYsailvk 154 y+de+r+e+ t h+Lr q e+ g++n+claDfvapk+sgv+Dy+G+Favtag+gi+e++++fea++ddY+ai++k lcl|FitnessBrowser__MR1:200213 1031 YTDETRTEVELTTHHLRMQLER-VGNDNFCLADFVAPKDSGVADYMGGFAVTAGHGIDEHVARFEANHDDYNAIMLK 1106 *******************987.799*************************************************** PP Met_synt_B12 155 aladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpacpdhtekktlfelldaeekigieLt 231 ladrLaeAfae++he+vrke+Wgya+de+l+ne+li+ekY+giRpApGYpacpdhtek l+ell+ +e+i++++t lcl|FitnessBrowser__MR1:200213 1107 CLADRLAEAFAERMHERVRKEFWGYAADEQLDNEALIREKYKGIRPAPGYPACPDHTEKGLLWELLKPNETIDLNIT 1183 ***************************************************************************** PP Met_synt_B12 232 eslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 es+am P+a+vsG+yfahp++ryF+v +i++dqvedyakrkg lcl|FitnessBrowser__MR1:200213 1184 ESYAMFPTAAVSGWYFAHPKSRYFGVSNIGRDQVEDYAKRKG 1225 ****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1244 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: 30.56 // [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