Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_013459006.1 SULKU_RS00740 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000183725.1:WP_013459006.1 Length = 1166 Score = 114 bits (286), Expect = 6e-30 Identities = 77/210 (36%), Positives = 117/210 (55%), Gaps = 18/210 (8%) Query: 13 LNDEDLVQQMFDDLYDGLKEE---IEESVNILLERGWAPYKVLTEALVGGMTIVGADFRD 69 L+DE+ + ++ L DG KE + E V + + +P K++ E L+ M +VG F Sbjct: 630 LSDEEKIAKL---LLDGDKERMIPLVERVRLTI----SPDKIVNEILIDAMKVVGELFGS 682 Query: 70 GILFVPEVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEG 129 G + +P VL +A MK + L P L++ ++VIGTVKGD+HD+GKNLV +++ Sbjct: 683 GKMQLPFVLQSAETMKTTVDYLNPYLSKQEKDTDTTLVIGTVKGDVHDVGKNLVDIILSN 742 Query: 130 AGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIV 189 GF+V++IGI +E YLE ++ +GMS LL + MK ++TM G V Sbjct: 743 NGFKVINIGIKTELEEYLEVMKSKDIHAIGMSGLLVKSTQVMKDNLETMAGMGITTP--V 800 Query: 190 LVGGAPLN----EEFGKAI--GADGYCRDA 213 L+GGA L ++F + I G YCRDA Sbjct: 801 LLGGAALTRSFVDDFCRPIYQGPIFYCRDA 830 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: 565 Number of extensions: 29 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: 1166 Length adjustment: 34 Effective length of query: 199 Effective length of database: 1132 Effective search space: 225268 Effective search space used: 225268 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