Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_013553448.1 NITSA_RS02460 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000186245.1:WP_013553448.1 Length = 1168 Score = 111 bits (278), Expect = 5e-29 Identities = 71/199 (35%), Positives = 109/199 (54%), Gaps = 11/199 (5%) Query: 13 LNDEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGIL 72 L+ E+ +Q++ L DG KE + V A +++ E L+ GM ++G F G + Sbjct: 633 LSTEEKIQKL---LMDGDKERLIPLVEEARHELGAD-RIVNEILIDGMKVIGELFGSGQM 688 Query: 73 FVPEVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGF 132 +P VL +A MK + L P L + ++VIGTVKGD+HD+GKNLV +++ GF Sbjct: 689 QLPFVLQSAETMKATVDYLNPYLTKQEKESDTTLVIGTVKGDVHDVGKNLVDIILSNNGF 748 Query: 133 EVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVG 192 +V +IGI +E +LEA EE D +GMS LL + MK ++ + +G + +++G Sbjct: 749 KVKNIGIKVELEQFLEAYEEVNADAIGMSGLLVKSTQVMKENLEELARRG--IEIPIIMG 806 Query: 193 GAPLNEEFGKAIGADGYCR 211 GA L F D YCR Sbjct: 807 GAALTRGF-----VDDYCR 820 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: 628 Number of extensions: 32 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 1168 Length adjustment: 34 Effective length of query: 199 Effective length of database: 1134 Effective search space: 225666 Effective search space used: 225666 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