Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_051958135.1 Q366_RS17575 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000745975.1:WP_051958135.1 Length = 814 Score = 141 bits (356), Expect = 3e-38 Identities = 83/211 (39%), Positives = 129/211 (61%), Gaps = 7/211 (3%) Query: 11 ADLNDEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDG 70 ADL ED Q+ D + G +E+IE N LE+G AP ++L + ++ + VG + Sbjct: 602 ADLPVED---QIVDAVIQGRREDIERLCNQALEKGIAPSELLEKKMIPAIMTVGEYYDAR 658 Query: 71 ILFVPEVLLAANAMKGGMAILKPLL-AETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEG 129 F+P+++ +A M+ G A+L+P L A G + G++V TV+GDIHDIGKN+V +M+ Sbjct: 659 KYFLPQLIASAETMQNGFAVLEPALNASGGNEKKGTLVFATVQGDIHDIGKNIVVLMLRN 718 Query: 130 AGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIV 189 GF+V+D+G + EN + A + H+ D++G+SAL+TTTM M VI E G + V Sbjct: 719 FGFDVIDLGKDVTAENIIAAAQTHKADLIGLSALMTTTMVRMPEVIALAKENGL--ECKV 776 Query: 190 LVGGAPLNEEFGKAIGADGYCRDAAVAVEMA 220 +VGGA + E+ ++IGA+ Y D AV +A Sbjct: 777 MVGGAVVTREWAESIGAE-YSSDGVEAVNVA 806 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: 412 Number of extensions: 22 Number of successful extensions: 3 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: 814 Length adjustment: 32 Effective length of query: 201 Effective length of database: 782 Effective search space: 157182 Effective search space used: 157182 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 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