Align candidate Ga0059261_0990 Ga0059261_0990 (methionine synthase (B12-dependent) (EC 2.1.1.13))
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.26909.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-121 388.5 0.0 1.4e-120 387.9 0.0 1.3 1 lcl|FitnessBrowser__Korea:Ga0059261_0990 Ga0059261_0990 methionine syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0990 Ga0059261_0990 methionine synthase (B12-dependent) (EC 2.1.1.13) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.9 0.0 1.4e-120 1.4e-120 1 273 [] 586 850 .. 586 850 .. 0.97 Alignments for each domain: == domain 1 score: 387.9 bits; conditional E-value: 1.4e-120 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAn 69 dl++l++yidWtpff+aWel+g+yp+il+d++vge+a++lf+dAq+mL+ki+eek+l+a++v+gl+p++ lcl|FitnessBrowser__Korea:Ga0059261_0990 586 DLADLRQYIDWTPFFRAWELAGNYPAILTDKVVGESATSLFADAQKMLDKIVEEKWLTARGVAGLWPCR 654 689****************************************************************** PP Met_synt_B12 70 segddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgieela 138 +egddi+v+ ++ e+++tl++Lrqq +k+eg++n+claDf+ + D+iG+Fav + +gie ++ lcl|FitnessBrowser__Korea:Ga0059261_0990 655 REGDDIIVHVED---EKHVTLPMLRQQIQKREGRANMCLADFIDRQ----GDWIGGFAVGI-HGIEPHL 715 ********6444...45789************************94....4**********.9****** PP Met_synt_B12 139 kefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApGYpac 207 ++f+++ ddYs+il+kaladrLaeAfae+lh+ vr+ lWgya+ e+l+ne+like+Y+giRpApGYpac lcl|FitnessBrowser__Korea:Ga0059261_0990 716 ARFKNAIDDYSDILLKALADRLAEAFAERLHHYVRTALWGYAEGEQLTNEALIKEEYRGIRPAPGYPAC 784 ********************************************************************* PP Met_synt_B12 208 pdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyakrkg 273 p+h+ k lf++lda++++gi+Ltes+am P+a+vsG+yf hp+a+yF+v+++++dq+e+ya+r+g lcl|FitnessBrowser__Korea:Ga0059261_0990 785 PEHSLKPILFDMLDAHKRTGISLTESFAMLPTAAVSGFYFGHPQAEYFGVARVGRDQLEEYATRRG 850 ****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (865 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: 00:00:00.01 # Mc/sec: 16.03 // [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