Align candidate WP_077278866.1 B1C78_RS09190 (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.11488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-134 433.0 0.0 5.2e-134 431.9 0.0 1.6 2 lcl|NCBI__GCF_002000365.1:WP_077278866.1 B1C78_RS09190 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077278866.1 B1C78_RS09190 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -4.2 0.0 0.5 0.5 40 67 .. 706 733 .. 704 735 .. 0.90 2 ! 431.9 0.0 5.2e-134 5.2e-134 1 273 [] 957 1230 .. 957 1230 .. 0.99 Alignments for each domain: == domain 1 score: -4.2 bits; conditional E-value: 0.5 Met_synt_B12 40 lfkdAqamLkkiieekllkakavvglfp 67 lf d++ +L +++++ ++ kav+ l+p lcl|NCBI__GCF_002000365.1:WP_077278866.1 706 LFGDGKMFLPQVVKSARVMKKAVAHLIP 733 8999************999999999876 PP == domain 2 score: 431.9 bits; conditional E-value: 5.2e-134 Met_synt_B12 1 dleelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 +leel +yidWtpff+aWel+ yp+i+ede+vgeeakklfkdA++mL+kii e +lka++v+g+fp lcl|NCBI__GCF_002000365.1:WP_077278866.1 957 PLEELKDYIDWTPFFHAWELHAAYPRIFEDEVVGEEAKKLFKDARDMLEKIIGEGWLKARGVIGFFP 1023 589**************************************************************** PP Met_synt_B12 68 Anseg.ddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglg 133 Ans++ ddie+y+de+r++ l++lh+Lrqq+e++ + pn claDf+ap+++ Dy+G+Favtag+g lcl|NCBI__GCF_002000365.1:WP_077278866.1 1024 ANSVDaDDIELYRDEDRKQPLMRLHHLRQQTERRGKGPNQCLADFIAPRDTALPDYLGAFAVTAGIG 1090 ***955************************************************************* PP Met_synt_B12 134 ieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRp 200 i+e++k+fea++ddY+ai++kaladrLaeAfae++he+vr+e+W ya++e+l+n++li+e+YqgiRp lcl|NCBI__GCF_002000365.1:WP_077278866.1 1091 IDEHVKRFEAAHDDYHAIMLKALADRLAEAFAERMHERVRREFWAYAPEEHLDNDALIREQYQGIRP 1157 ******************************************************************* PP Met_synt_B12 201 ApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqved 267 ApGYpacp+htek l+elld e++g+++tes+am P+a+vsG+yfahpea+yF+vgki++dqv++ lcl|NCBI__GCF_002000365.1:WP_077278866.1 1158 APGYPACPEHTEKGLLWELLDPVENAGMSITESYAMLPTAAVSGWYFAHPEAKYFNVGKINRDQVAS 1224 ******************************************************************* PP Met_synt_B12 268 yakrkg 273 yakrkg lcl|NCBI__GCF_002000365.1:WP_077278866.1 1225 YAKRKG 1230 ****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1250 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 19.30 // [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