Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_012852642.1 TCUR_RS11345 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000024385.1:WP_012852642.1 Length = 1157 Score = 121 bits (304), Expect = 5e-32 Identities = 72/224 (32%), Positives = 126/224 (56%), Gaps = 11/224 (4%) Query: 16 EDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVP 75 E L +++ D +G++ +++E++ + +++ + L+ GM VG F G + +P Sbjct: 641 ERLKRRIIDGEANGMEADLDEAL-----QSRPALEIINDVLLDGMKTVGDLFGSGQMQLP 695 Query: 76 EVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVV 135 VL +A MK +A L+P + ++ G +V+ TVKGD+HDIGKNLV +++ G+EV+ Sbjct: 696 FVLQSAEVMKAAVAYLEPHMEKSADGGKGRIVLATVKGDVHDIGKNLVDIILSNNGYEVI 755 Query: 136 DIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAP 195 ++GI P+ +EA +EH+ D++GMS LL + MK ++ + +G + VL+GGA Sbjct: 756 NLGIKQPISAIVEAAKEHRADVIGMSGLLVKSTVVMKENLEELNARGLARQWPVLLGGAA 815 Query: 196 LNEEFGKAIGA---DG---YCRDAAVAVEMAKDFVARKHNQMSA 233 L + + A DG Y RDA + + F+A K + A Sbjct: 816 LTRAYVEQDLAELFDGEVRYARDAFEGLRLMDAFMAVKRGEEGA 859 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: 573 Number of extensions: 25 Number of successful extensions: 1 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: 1157 Length adjustment: 34 Effective length of query: 199 Effective length of database: 1123 Effective search space: 223477 Effective search space used: 223477 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