Align candidate WP_011612063.1 TERY_RS11900 (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.23169.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-38 118.6 0.0 3.1e-38 117.8 0.0 1.4 1 lcl|NCBI__GCF_000014265.1:WP_011612063.1 TERY_RS11900 methionine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011612063.1 TERY_RS11900 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.8 0.0 3.1e-38 3.1e-38 2 256 .. 968 1223 .. 967 1224 .] 0.88 Alignments for each domain: == domain 1 score: 117.8 bits; conditional E-value: 3.1e-38 Met_synt_B12 2 leelveyidWtpffq.aWelkgkypkiledekvgeeakklfkdAqamLkkiieekllkakavvglfp 67 leel y+d + f+ W++++ + ++e a+k++ ++ +k+ +e++l+ v+g fp lcl|NCBI__GCF_000014265.1:WP_011612063.1 968 LEELFWYMDLQALFAgQWQFRKP-KGQPREEYDWFLASKVYPILEEWKQKVRTEQWLEPTLVYGYFP 1033 78888999998877647998876.344455556668999999999999******************* PP Met_synt_B12 68 Ansegddievyadesrse...elatlhtLrqqaekeegkpnlclaDfvapkesgvkDyiGlFavtag 131 + + g+ ++vy+ + ++ ++ +++ ++++ lc+aDf++p e+++ D++ + avt+g lcl|NCBI__GCF_000014265.1:WP_011612063.1 1034 CAAIGNSVHVYDPSVIEQgltPTTATPFVTWTFPRQKSMRRLCIADFIRPLEHDQFDVLPMQAVTMG 1100 **********9555533333345567777777777778889************************** PP Met_synt_B12 132 lgieelakefeaekddYsailvkaladrLaeAfaellhekvrkelWgyakdeklsneelikekYqgi 198 + ++a+e+ + ++ + + + +a +LaeA+ae+ h+++r+e gy e +++++++++Yqg lcl|NCBI__GCF_000014265.1:WP_011612063.1 1101 EIATQKAQELYQGNEYTNYLYFHGMAVQLAEALAEWSHARIRRE-LGYGDLEPDNIRDILAQRYQGS 1166 ********99999777788999*********************9.6********************* PP Met_synt_B12 199 RpApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahpearyFa 256 R+++GYpacp + +ll a++ ig+++ es ++P+++ ++++ hp aryF+ lcl|NCBI__GCF_000014265.1:WP_011612063.1 1167 RYSFGYPACPVVIDQVPQLQLLGADR-IGVSIDESEQLYPEQTTTAFVIYHPVARYFS 1223 *************************9.******************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (1224 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: 21.62 // [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