Align candidate WP_028583363.1 G494_RS0103145 (5-methyltetrahydrofolate--homocysteine methyltransferase)
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.28004.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-39 121.4 0.0 4.4e-39 120.6 0.0 1.4 1 lcl|NCBI__GCF_000429965.1:WP_028583363.1 G494_RS0103145 5-methyltetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429965.1:WP_028583363.1 G494_RS0103145 5-methyltetrahydrofolate--homocysteine methyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 120.6 0.0 4.4e-39 4.4e-39 45 257 .. 616 816 .] 590 816 .] 0.91 Alignments for each domain: == domain 1 score: 120.6 bits; conditional E-value: 4.4e-39 Met_synt_B12 45 qamLkkiieekllkakavvglfpAnsegddievyadesrseelatlhtLrqqaekeegkpnlclaDfva 113 q ++++ +e l++ k +g fp+ ++++ ++v + +l+ + + rqq ++p+lc+aD+ + lcl|NCBI__GCF_000429965.1:WP_028583363.1 616 QGLIRRSLDEGLIRPKVSYGYFPCYAQEETVMVE----VEGSLHPFAFPRQQ-----EQPHLCIADYFK 675 557788889999*******************994....344578899*****.....569********* PP Met_synt_B12 114 pkesgvkDyiGlFavtaglgieelakefeaekddYsa.ilvkaladrLaeAfaellhekvrkelWgyak 181 +e+g D G+F+vt+g + + ++++ ++ d Y++ ++++ + +++A+ae+ h +r e g a lcl|NCBI__GCF_000429965.1:WP_028583363.1 676 TREEG-GDIAGFFIVTIGERMGQETARLYEA-DRYHDyLMLHGFSVEVTDALAEYWHGVMRSE-LGIAG 741 *9998.7**************9999999888.77764399******************99998.69999 PP Met_synt_B12 182 deklsneelikekYqgiRpApGYpacpdhtekktlfelldaeekigieLteslamtPaasvsGlyfahp 250 + +l++++Yqg R+ +GYpacpd + +k lf++l+ e+ ig++Lte++ m+P+++ s++++ hp lcl|NCBI__GCF_000429965.1:WP_028583363.1 742 ADPTAGGSLVSQNYQGSRYGFGYPACPDMEVHKPLFSFLKPEK-IGVSLTENMQMVPEQTTSAIVVHHP 809 999999************************************9.************************* PP Met_synt_B12 251 earyFav 257 +a+yFav lcl|NCBI__GCF_000429965.1:WP_028583363.1 810 QAKYFAV 816 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (273 nodes) Target sequences: 1 (816 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15.42 // [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