Align candidate WP_106717619.1 CU100_RS16195 (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.2153415.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-129 416.2 0.0 4.9e-129 415.6 0.0 1.3 1 NCBI__GCF_003010935.1:WP_106717619.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106717619.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.6 0.0 4.9e-129 4.9e-129 1 273 [] 960 1232 .. 960 1232 .. 0.99 Alignments for each domain: == domain 1 score: 415.6 bits; conditional E-value: 4.9e-129 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAnse 71 dl+e+++yidWtpffq+Welkg+yp+il+d+k+ge+a++lf+dAqamLkkii+ek+++ kavvgl+pA ++ NCBI__GCF_003010935.1:WP_106717619.1 960 DLAEIARYIDWTPFFQTWELKGRYPAILDDDKQGEAARQLFDDAQAMLKKIIAEKWFNPKAVVGLWPAGTV 1030 699******************************************************************** PP Met_synt_B12 72 gddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgieelakefe 142 gddi v+ade+rseelat++tLrqq +k++g+pn++l+Df+ap++s vkDy+G+F+vtag++ ++a++fe NCBI__GCF_003010935.1:WP_106717619.1 1031 GDDIRVFADERRSEELATFYTLRQQLSKRDGRPNVALSDFIAPEDSAVKDYMGAFVVTAGIEEIAIAERFE 1101 *********************************************************************** PP Met_synt_B12 143 aekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpacpdhtek 213 +++ddYs+ilvkaladr+aeAfael+he+vrke+W ya+de+ls eeli e Y+giRpApGYpa+pdhtek NCBI__GCF_003010935.1:WP_106717619.1 1102 RANDDYSSILVKALADRFAEAFAELMHERVRKEFWSYAPDENLSPEELIGEPYRGIRPAPGYPAQPDHTEK 1172 *********************************************************************** PP Met_synt_B12 214 ktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 +tlf++ldae++i+++Ltes+am+P +svsG+y+ hpe+ yF+v+k+e+dqvedy rk+ NCBI__GCF_003010935.1:WP_106717619.1 1173 ATLFRILDAEAQINVRLTESFAMWPGSSVSGIYIGHPESYYFGVAKVERDQVEDYSVRKQ 1232 *********************************************************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1258 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 46.20 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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