Align candidate WP_012501603.1 CPAR_RS01790 (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.6836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-129 414.8 0.0 1.9e-128 413.7 0.0 1.6 2 lcl|NCBI__GCF_000020505.1:WP_012501603.1 CPAR_RS01790 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012501603.1 CPAR_RS01790 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -4.0 0.0 0.44 0.44 39 67 .. 702 730 .. 698 737 .. 0.86 2 ! 413.7 0.0 1.9e-128 1.9e-128 3 273 .] 939 1208 .. 937 1208 .. 0.99 Alignments for each domain: == domain 1 score: -4.0 bits; conditional E-value: 0.44 Met_synt_B12 39 klfkdAqamLkkiieekllkakavvglfp 67 +lf++++ +L +++++ ++ + v+ l+p lcl|NCBI__GCF_000020505.1:WP_012501603.1 702 DLFAEGKMFLPQVVKSARVMKRSVAVLVP 730 6999************9999999999887 PP == domain 2 score: 413.7 bits; conditional E-value: 1.9e-128 Met_synt_B12 3 eelveyidWtpffqaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfpAn 69 l++yidWtpff++Wel+g yp+iledekvgeea+klf+dA+a+L++i +ekll +k+v+g+fpAn lcl|NCBI__GCF_000020505.1:WP_012501603.1 939 GALRSYIDWTPFFRSWELHGVYPQILEDEKVGEEATKLFNDATALLDRIDSEKLLGIKGVAGIFPAN 1005 5799*************************************************************** PP Met_synt_B12 70 segddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgiee 136 s gddi vy+d++rs ++lhtLrqq+ek +g++nl+laDfvap+esgv+D+iG+F+vtaglgi++ lcl|NCBI__GCF_000020505.1:WP_012501603.1 1006 SIGDDIFVYSDDERSMIRTVLHTLRQQSEK-HGEANLALADFVAPRESGVNDWIGCFTVTAGLGIQS 1071 ***************************998.799********************************* PP Met_synt_B12 137 lakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpApG 203 l++ef ae+ddY++i+++aladrLaeAfae+lhekvr+elWgya+ e l eeli+e+Y+giRpApG lcl|NCBI__GCF_000020505.1:WP_012501603.1 1072 LLQEFAAENDDYHRIMTQALADRLAEAFAEMLHEKVRRELWGYAPGEILGSEELIAEQYRGIRPAPG 1138 ******************************************************************* PP Met_synt_B12 204 YpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFavgkiekdqvedyak 270 Ypacpdhtek+t+f+ll+ae+++g++Lte++am Paasv+Glyfa+p+++yF +gki+kdqvedya+ lcl|NCBI__GCF_000020505.1:WP_012501603.1 1139 YPACPDHTEKATIFDLLNAEAATGVTLTETFAMNPAASVCGLYFANPASKYFVLGKIGKDQVEDYAN 1205 ******************************************************************* PP Met_synt_B12 271 rkg 273 rkg lcl|NCBI__GCF_000020505.1:WP_012501603.1 1206 RKG 1208 *97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1227 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: 26.56 // [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