Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate SMc04331 SMc04331 dimethylamine corrinoid protein
Query= reanno::Phaeo:GFF1319 (233 letters) >FitnessBrowser__Smeli:SMc04331 Length = 232 Score = 375 bits (963), Expect = e-109 Identities = 185/228 (81%), Positives = 205/228 (89%) Query: 6 DDIILADLNDEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGA 65 D+IIL DL+DE+LVQQM DDLYDGLKEEIEE ILL+RGW PY VLT+ALV GM IVG Sbjct: 4 DEIILEDLSDEELVQQMHDDLYDGLKEEIEEGTRILLKRGWTPYDVLTQALVEGMRIVGI 63 Query: 66 DFRDGILFVPEVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSM 125 DFRDGILFVPEVLL+ANAMK GM IL+PLL ETGAP++G MVIGTVKGDI DIGKNLV M Sbjct: 64 DFRDGILFVPEVLLSANAMKAGMFILRPLLVETGAPKLGKMVIGTVKGDIDDIGKNLVGM 123 Query: 126 MMEGAGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRD 185 MMEGAGF+VVD+GINNPVENYLEALE +PDILGMSALLTTTMPYMKVVIDTM E+G RD Sbjct: 124 MMEGAGFDVVDLGINNPVENYLEALEREKPDILGMSALLTTTMPYMKVVIDTMKEKGLRD 183 Query: 186 DYIVLVGGAPLNEEFGKAIGADGYCRDAAVAVEMAKDFVARKHNQMSA 233 +Y+VLVGGAPLNEEFGKA+GAD YCRDAAVAVE AKD++ RKHNQ++A Sbjct: 184 EYVVLVGGAPLNEEFGKAVGADAYCRDAAVAVETAKDYMKRKHNQLAA 231 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: 255 Number of extensions: 2 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: 232 Length adjustment: 23 Effective length of query: 210 Effective length of database: 209 Effective search space: 43890 Effective search space used: 43890 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 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