Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_012675280.1 PERMA_RS08280 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000021565.1:WP_012675280.1 Length = 1182 Score = 125 bits (314), Expect = 4e-33 Identities = 80/222 (36%), Positives = 128/222 (57%), Gaps = 14/222 (6%) Query: 3 EDADDIILADLNDEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTI 62 ED DD +DL E+ ++++ L DG KE++ ++V P K++ E L+ M + Sbjct: 621 EDQDDF--SDLPVEERIKKL---LIDGEKEKLIKTVEEA-RHSIPPEKIINEVLIDAMKV 674 Query: 63 VGADFRDGILFVPEVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNL 122 VG F +G + +P VL +A AMK + L L + + ++++GTVKGD+HD+GKNL Sbjct: 675 VGDLFGEGKMQLPFVLQSAEAMKAAVDYLNQYLPKKKKEKETTLILGTVKGDVHDVGKNL 734 Query: 123 VSMMMEGAGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQG 182 V +++ GF+VV+IGI +E++++A +EH D +GMS LL + MK ++ M ++G Sbjct: 735 VDIILTNNGFKVVNIGIKAELEDFIKAYKEHNADAIGMSGLLVKSTLEMKNNLEEMRKRG 794 Query: 183 KRDDYIVLVGGAPLNEEFGKAI------GADGYCRDAAVAVE 218 + VL+GGA LN+ F G YCRDA +E Sbjct: 795 --INVPVLLGGAALNKSFVDQYCRPVYDGPVFYCRDAFDGIE 834 Lambda K H 0.318 0.138 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 664 Number of extensions: 37 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 1182 Length adjustment: 35 Effective length of query: 198 Effective length of database: 1147 Effective search space: 227106 Effective search space used: 227106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
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