Align candidate WP_043743213.1 AMB_RS02225 (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.16999.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-52 164.1 0.0 3.4e-52 163.6 0.0 1.2 1 lcl|NCBI__GCF_000009985.1:WP_043743213.1 AMB_RS02225 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043743213.1 AMB_RS02225 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 163.6 0.0 3.4e-52 3.4e-52 2 257 .. 911 1157 .] 910 1157 .] 0.92 Alignments for each domain: == domain 1 score: 163.6 bits; conditional E-value: 3.4e-52 Met_synt_B12 2 leelveyidWtpffqa.WelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 l++l+++++ t+ +q+ W+ +++ ++i e ++ + k++ A +mLk+ +e+ l+ +av+g ++ lcl|NCBI__GCF_000009985.1:WP_043743213.1 911 LQNLIPFLNETMLYQFhWGYRKQGKSIEE--FKAWAHKEIRPVAMDMLKRCAKEEILRPQAVYGYWK 975 78899999999988854888888777755..55778899999************************* PP Met_synt_B12 68 AnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 A s++d ++++a++ ++e+a++++ rq + + lc+aDf +p ++ v+D+iGl +vt+g + lcl|NCBI__GCF_000009985.1:WP_043743213.1 976 AASDNDSVVLFAEDG-TTEVARFPFPRQAK-----DGGLCIADFFRPVSDPVRDVIGLQVVTMGKRA 1036 **********97666.55689******993.....458***************************** PP Met_synt_B12 135 eelakefeaekddYsa.ilvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRp 200 e+a+++ ++ d+Y++ + ++ l+ +aeA+ae++h+++r e g+a++++ ++++l+k++Y+g R lcl|NCBI__GCF_000009985.1:WP_043743213.1 1037 TEVAQDWFKA-DKYQDyLYLHGLSVEMAEAMAEYVHKRIRSE-LGFAAEDAADMDRLLKQNYRGSRF 1101 *******999.99987256899*******************9.6*********************** PP Met_synt_B12 201 ApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFav 257 ++GYpacp + +++l +ll ae+ ig++L+e++ + P++s s+++ hp+a+yF+v lcl|NCBI__GCF_000009985.1:WP_043743213.1 1102 SFGYPACPRIEDQTQLLSLLGAER-IGVTLSEEFQLEPEQSTSAIVTVHPQAKYFSV 1157 ***********************9.******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1157 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 19.56 // [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