Align candidate WP_092998959.1 BLP65_RS15270 (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.11370.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-130 420.7 0.1 2.8e-130 419.7 0.1 1.5 2 lcl|NCBI__GCF_900102855.1:WP_092998959.1 BLP65_RS15270 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092998959.1 BLP65_RS15270 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.9 0.0 0.39 0.39 39 67 .. 725 753 .. 722 756 .. 0.90 2 ! 419.7 0.1 2.8e-130 2.8e-130 2 272 .. 994 1265 .. 993 1266 .. 0.99 Alignments for each domain: == domain 1 score: -3.9 bits; conditional E-value: 0.39 Met_synt_B12 39 klfkdAqamLkkiieekllkakavvglfp 67 +lf d++ +L +++++ ++ kav+ l+p lcl|NCBI__GCF_900102855.1:WP_092998959.1 725 DLFGDGKMFLPQVVKSARVMKKAVAHLIP 753 6899*************9*9999999886 PP == domain 2 score: 419.7 bits; conditional E-value: 2.8e-130 Met_synt_B12 2 leelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpA 68 l++lv+yidWt+ff+aWelkg +p+iled+++geeakkl++dA+ mL+++i+ek+l+a a vg++pA lcl|NCBI__GCF_900102855.1:WP_092998959.1 994 LQTLVPYIDWTFFFHAWELKGVFPRILEDKEKGEEAKKLYTDARGMLEQLIAEKWLHAAAQVGIYPA 1060 899**************************************************************** PP Met_synt_B12 69 nse.gddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 ns+ +dd+e+y+de+r+e+l+t+h+Lrqq+ek+ g+pn ++aDfvapkesg+kDy+G+Fa+t+glgi lcl|NCBI__GCF_900102855.1:WP_092998959.1 1061 NSVdHDDVELYQDEERTEVLTTFHFLRQQSEKRPGQPNKSMADFVAPKESGKKDYLGGFACTTGLGI 1127 **956************************************************************** PP Met_synt_B12 135 eelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpA 201 +e+++efea++ddY+ai++kaladrLaeA+ae+lh++vrk++Wgya+de+l+ne+like+YqgiRpA lcl|NCBI__GCF_900102855.1:WP_092998959.1 1128 DEKVAEFEAAHDDYNAIMLKALADRLAEACAEWLHQQVRKTIWGYAEDENLDNESLIKEQYQGIRPA 1194 ******************************************************************* PP Met_synt_B12 202 pGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedy 268 GYpacpdhtek tl++ll+ +++ig++Ltes am+P+a+vsGlyf+ p+++yFavgk++++qv++y lcl|NCBI__GCF_900102855.1:WP_092998959.1 1195 LGYPACPDHTEKDTLWSLLQPDQAIGLTLTESKAMVPTAAVSGLYFSAPDSSYFAVGKLDREQVAQY 1261 ******************************************************************* PP Met_synt_B12 269 akrk 272 a+rk lcl|NCBI__GCF_900102855.1:WP_092998959.1 1262 AERK 1265 ***9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1284 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: 24.18 // [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