Align candidate YP_001328535.1 Smed_2870 (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.29355.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-128 414.2 0.1 2e-128 413.6 0.1 1.3 1 lcl|NCBI__GCF_000017145.1:YP_001328535.1 Smed_2870 B12-dependent methioni Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001328535.1 Smed_2870 B12-dependent methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.6 0.1 2e-128 2e-128 1 273 [] 959 1231 .. 959 1231 .. 0.99 Alignments for each domain: == domain 1 score: 413.6 bits; conditional E-value: 2e-128 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 dl+el++yidWtpffq+We+kg yp+il+de++g++a++lf+dAqamL++i++ek++ kavvg++p lcl|NCBI__GCF_000017145.1:YP_001328535.1 959 DLAELARYIDWTPFFQTWEMKGVYPRILDDEHQGAAARQLFEDAQAMLAQIVAEKWFAPKAVVGFWP 1025 699**************************************************************** PP Met_synt_B12 68 AnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 A s+gdd+ +++de+r+ elatl tLrqq k++g+pn++laDfvap+esg++Dy G+F+vtag++ lcl|NCBI__GCF_000017145.1:YP_001328535.1 1026 AGSVGDDVRLFTDETRKGELATLFTLRQQLVKRDGRPNVALADFVAPAESGKRDYAGAFVVTAGIEE 1092 ******************************************************************* PP Met_synt_B12 135 eelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpA 201 ++a++fe+++ddYs+i+vkaladr+aeAfae++he vrkelWgya+de+++ +eli e Y giRpA lcl|NCBI__GCF_000017145.1:YP_001328535.1 1093 VAIAERFERANDDYSSIMVKALADRFAEAFAERMHEYVRKELWGYAADEAFTPQELIGEPYAGIRPA 1159 ******************************************************************* PP Met_synt_B12 202 pGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedy 268 pGYpa+pdhtek+tlf+ll+ae++ig++Ltes+am+P +svsGly+ hp++ yF+v+kie+dqvedy lcl|NCBI__GCF_000017145.1:YP_001328535.1 1160 PGYPAQPDHTEKETLFRLLNAEAAIGVKLTESYAMWPGSSVSGLYIGHPDSYYFGVAKIERDQVEDY 1226 ******************************************************************* PP Met_synt_B12 269 akrkg 273 a+rk+ lcl|NCBI__GCF_000017145.1:YP_001328535.1 1227 AERKQ 1231 ***95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1257 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 34.67 // [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