Align candidate WP_084544571.1 H566_RS21925 (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.23325.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-120 386.8 0.0 6.1e-120 385.8 0.0 1.5 2 lcl|NCBI__GCF_000482785.1:WP_084544571.1 H566_RS21925 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_084544571.1 H566_RS21925 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.7 0.0 0.36 0.36 40 77 .. 403 441 .. 401 458 .. 0.72 2 ! 385.8 0.0 6.1e-120 6.1e-120 1 264 [. 644 910 .. 644 911 .] 0.97 Alignments for each domain: == domain 1 score: -3.7 bits; conditional E-value: 0.36 Met_synt_B12 40 lfkdAqamLkkiieekllkakavvglfpAnse.gddiev 77 lf +++ +L +++++ ++ +av+ l+p +e + +ie lcl|NCBI__GCF_000482785.1:WP_084544571.1 403 LFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEeKRQIEA 441 778888899999999999999999998866552345555 PP == domain 2 score: 385.8 bits; conditional E-value: 6.1e-120 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAn 69 dl+el++yidW pffq+W+l+g +p++l+d++vge+a+k+f+d+qamLkk+i+ ++l+a+avvg++pAn lcl|NCBI__GCF_000482785.1:WP_084544571.1 644 DLAELARYIDWGPFFQTWDLHGAFPALLDDPVVGESARKVFADGQAMLKKLIDGRQLNASAVVGFWPAN 712 699****************************************************************** PP Met_synt_B12 70 seg.ddievyades...rseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 s+g + i++y+d++ ++++l +++ Lrqq++k+eg +n claD++ap +sgv+DyiG+Favtaglg+ lcl|NCBI__GCF_000482785.1:WP_084544571.1 713 SDGaETITLYTDDDardEAHVLFRWKNLRQQTAKREGVENKCLADYIAPLDSGVRDYIGVFAVTAGLGA 781 **8688****99984333446788********************************************* PP Met_synt_B12 135 eelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApG 203 ++la+++ea++ddYsai+vkaladrLaeAfae +he+vrk+lWgya+de+l+neelikekY giRpApG lcl|NCBI__GCF_000482785.1:WP_084544571.1 782 DKLAERYEAAHDDYSAIMVKALADRLAEAFAEAMHERVRKDLWGYAPDEALTNEELIKEKYVGIRPAPG 850 ********************************************************************* PP Met_synt_B12 204 YpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdq 264 Ypacp h+ k+++f lda++ ig+ Ltes+amtPa+svsG+y++hp+a+yF+vg+i+++q lcl|NCBI__GCF_000482785.1:WP_084544571.1 851 YPACPRHEVKREMFAALDATA-IGMGLTESFAMTPASSVSGFYLSHPKAQYFNVGEIGDEQ 910 *********************.*************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (911 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: 16.41 // [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