Align [corrinoid iron-sulfur protein]-dependent methionine synthase (characterized)
to candidate WP_005814543.1 DHAF_RS11500 hypothetical protein
Query= metacyc::MONOMER-21502 (342 letters) >NCBI__GCF_000021925.1:WP_005814543.1 Length = 357 Score = 179 bits (453), Expect = 1e-49 Identities = 112/348 (32%), Positives = 169/348 (48%), Gaps = 21/348 (6%) Query: 8 FLPTMIGSMPHTDPKAAVDIITHYLQDIPVWPQLPRRSCLEGMSAQFSQGLPGVK----I 63 FL T +GS+P+ + A+ I L P WPQLP+ Q+ + L Sbjct: 11 FLATGVGSLPYAQAETALSQIWKALPQAPHWPQLPQLGAESSFVGQYLKVLIETGCIGGF 70 Query: 64 NQDKVWIEPNPSFESELESLYQAYLD------NDFNKFPIGAEYAAGLYELAS-----RN 112 Q + ++ P + + Y+ YL N +F E G E Sbjct: 71 EQPRFQVDA-PDWTERMAHFYEYYLHAEAGDPNALAEFGFTPEGGLGFNEFCDVLDQQGT 129 Query: 113 LSPLLVKGHITGPLTYCMSIKDPSGKDILYDEVLSDAATKLLKLKATWQEHFLRNICRNT 172 LL+KG ++GP+T M I DP+ K YD+ D K L+ A WQ L Sbjct: 130 QEALLLKGQLSGPVTLGMQITDPNRKAAYYDDFQRDILVKSLRCHARWQTKRLAQYGLPV 189 Query: 173 IIFVDEPAMSAYG-SAYLPLSREQVTGMFDEVFSGI---SGLKGVHCCGNTDWSILMDTR 228 ++ +D+P + AYG S +L L R + +EV GI G+ G H C DW++L D++ Sbjct: 190 LMSIDDPGLYAYGASTHLTLDRTVLIENINEVAEGILAEGGIPGAHVCAGMDWTLLFDSK 249 Query: 229 VDIINFDTYAYANSLSIYTDEVKAFIKRGGAVAWGIVPTDEKALKEETAASLKDRLEAAM 288 + ++NFD Y Y S+++ + ++ F+++GG ++WGIVPT KA E+AASL++RLE + Sbjct: 250 IRVVNFDAYEYMTSMAVLAEPLERFLQKGGILSWGIVPTSAKAW-GESAASLRERLETNI 308 Query: 289 SHFDSHGLPFAELARHSLITPACGLGLKSPEAAERAPQLLAELSALLR 336 G+ L S++TP+CG G E AER LL ELS R Sbjct: 309 KELTKRGVSEDRLRSQSMLTPSCGTGTLDIELAERIYALLQELSTSYR 356 Lambda K H 0.319 0.135 0.409 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: 324 Number of extensions: 15 Number of successful extensions: 4 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: 342 Length of database: 357 Length adjustment: 29 Effective length of query: 313 Effective length of database: 328 Effective search space: 102664 Effective search space used: 102664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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