Align candidate WP_078430828.1 BK574_RS10060 (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.28058.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-63 201.0 0.0 5.4e-63 199.0 0.0 2.0 2 lcl|NCBI__GCF_002019605.1:WP_078430828.1 BK574_RS10060 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430828.1 BK574_RS10060 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.6 0.1 0.17 0.17 31 64 .. 835 868 .. 827 886 .. 0.77 2 ! 199.0 0.0 5.4e-63 5.4e-63 2 257 .. 897 1144 .. 896 1146 .. 0.96 Alignments for each domain: == domain 1 score: -2.6 bits; conditional E-value: 0.17 Met_synt_B12 31 ekvgeeakklfkdAqamLkkiieekllkakavvg 64 ++++e kkl +d q+ L+++ +e++ k ++v+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 835 LVKEDELKKLEEDKQTKLQQVGNEETEKKNKVTT 868 5667789999999999999999998888777765 PP == domain 2 score: 199.0 bits; conditional E-value: 5.4e-63 Met_synt_B12 2 leelveyidWtpff.qaWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 +++l +yi+ ++ + +l+gk ++l + e+a++l ++ ++L + +++ ll+a++++++fp lcl|NCBI__GCF_002019605.1:WP_078430828.1 897 ISHLEPYINLQMLLgKHLGLHGKVSRLLAEG--DEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFP 961 7889999999998835679*****9999965..78999***************************** PP Met_synt_B12 68 AnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtaglgi 134 A+s+g+di++y+ +++++e++++ + rq+ ++p lclaD+v++ +sg+ Dy+G++avtag+g+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 962 AQSKGNDIIIYDPQDEKTEIERFSFPRQN-----HEPFLCLADYVRSIDSGEMDYVGFLAVTAGIGV 1023 ***********99999999********99.....469****************************** PP Met_synt_B12 135 eelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgiRpA 201 +e+a + ++e d + l++a a Lae fae+ h+ +r++ Wg+ +l++ + ++ kYqg+R + lcl|NCBI__GCF_002019605.1:WP_078430828.1 1024 REKAMKAKDEGDYLFSHLIQATALELAEGFAERTHQLIRDQ-WGFPDPVELTMVDRFSAKYQGVRVS 1089 *************9*************************86.************************* PP Met_synt_B12 202 pGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFav 257 +GYpacp+ + +++lf+ll+ e+ igi+Lte+++m P+asv +++f+hpe ryF+v lcl|NCBI__GCF_002019605.1:WP_078430828.1 1090 FGYPACPNLEDQAKLFKLLQPEK-IGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144 **********************9.******************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1148 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: 20.97 // [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