Align candidate WP_015817782.1 TERTU_RS09440 (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.4072.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-124 398.5 0.0 1.4e-123 397.7 0.0 1.4 1 lcl|NCBI__GCF_000023025.1:WP_015817782.1 TERTU_RS09440 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015817782.1 TERTU_RS09440 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.7 0.0 1.4e-123 1.4e-123 2 273 .] 942 1211 .. 941 1211 .. 0.97 Alignments for each domain: == domain 1 score: 397.7 bits; conditional E-value: 1.4e-123 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpA 68 l+elveyidWtpff +W+l gk+p+il+d++vge+a++l++dA+a+L++i++ kll+aka++g+++A lcl|NCBI__GCF_000023025.1:WP_015817782.1 942 LTELVEYIDWTPFFITWDLVGKFPAILTDKVVGEAATSLYQDARALLQDIVDGKLLQAKAILGFWEA 1008 89***************************************************************** PP Met_synt_B12 69 nse.gddievyadesrseelatlhtLrqqaeke.egkpnlclaDfvapkesgvkDyiGlFavtaglg 133 n++ +ddi+++ +++e +atlh++rqq k+ ++k+ l+laDf+ap+esgv+D +G+F vtag+g lcl|NCBI__GCF_000023025.1:WP_015817782.1 1009 NTVdHDDIVLT---HNAEPIATLHHIRQQVIKNdNDKHLLSLADFIAPQESGVTDFVGGFSVTAGIG 1072 **95699**95...556799*********98884666779*************************** PP Met_synt_B12 134 ieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRp 200 ++ela++++a+ ddY+ai+vkaladrLaeAfae+lhe+vrke+Wgy + e+l+++eli+ekY+giRp lcl|NCBI__GCF_000023025.1:WP_015817782.1 1073 ADELAASYQAKGDDYNAIMVKALADRLAEAFAEHLHERVRKEFWGYDSAEALDKDELIREKYRGIRP 1139 ******************************************************************* PP Met_synt_B12 201 ApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqved 267 ApGYpacpdhtek+tlf+ll+a++ ig++Lte++am PaasvsG+yf+hpe++yF+vgki++dqve+ lcl|NCBI__GCF_000023025.1:WP_015817782.1 1140 APGYPACPDHTEKATLFKLLQADR-IGVSLTEHYAMFPAASVSGWYFSHPESQYFNVGKISRDQVES 1205 ***********************9.****************************************** PP Met_synt_B12 268 yakrkg 273 a+rkg lcl|NCBI__GCF_000023025.1:WP_015817782.1 1206 LAERKG 1211 ****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1229 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: 00:00:00.10 # Mc/sec: 3.12 // [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