Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate H281DRAFT_02076 H281DRAFT_02076 methionine synthase (B12-dependent)
Query= reanno::Phaeo:GFF1319 (233 letters) >FitnessBrowser__Burk376:H281DRAFT_02076 Length = 900 Score = 100 bits (249), Expect = 1e-25 Identities = 64/178 (35%), Positives = 95/178 (53%), Gaps = 19/178 (10%) Query: 32 EEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMKGGMAIL 91 E+ EE + G P V+ L+ GM IVG F G +F+P+V+ +A MK +A L Sbjct: 335 EDTEEVRAKIAAAGGRPINVIEGPLMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHL 394 Query: 92 KPLLAET---------GAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNP 142 P + E G +VI TVKGD+HDIGKN+VS++++ FEVV++G+ P Sbjct: 395 IPFIEEEKKQLAAAGGDVRAKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVP 454 Query: 143 VENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYI------VLVGGA 194 + L + DI+G+S L+T ++ M V M +RDDY +L+GGA Sbjct: 455 CNDILAKAKVEGADIIGLSGLITPSLEEMAYVASEM----QRDDYFRVKKIPLLIGGA 508 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: 458 Number of extensions: 26 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: 900 Length adjustment: 33 Effective length of query: 200 Effective length of database: 867 Effective search space: 173400 Effective search space used: 173400 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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