Align [corrinoid iron-sulfur protein]-dependent methionine synthase (characterized)
to candidate WP_013706058.1 DESAC_RS05370 hypothetical protein
Query= metacyc::MONOMER-21502 (342 letters) >NCBI__GCF_000195295.1:WP_013706058.1 Length = 351 Score = 241 bits (615), Expect = 2e-68 Identities = 138/333 (41%), Positives = 195/333 (58%), Gaps = 12/333 (3%) Query: 11 TMIGSMPHTDPKAAVDIITHYLQDIPVWPQLPRRSCLEGMSAQFSQGLPGVKINQDK--V 68 T IGS P D AA +I L ++P WPQLP++ LE M Q + GLP ++++ ++ V Sbjct: 10 TGIGSTPFWDSHAAARLILENLTEMPFWPQLPQKGFLEDMVPQGAGGLPLMQLDSEQRLV 69 Query: 69 WIEPNPSFESELESLYQAYLDNDFNKFPIGAEYAAGLYEL-----ASRNLSPLLVKGHIT 123 ++ E L Y+A L D ++F + + A+G Y L AS P VKG I Sbjct: 70 RLDERADREEGLTDFYEAVLQLDLDRFGLSPDEASGFYALLEELPASGGGGPEYVKGQIV 129 Query: 124 GPLTYCMSIKDPSGKDILYDEVLSDAATKLLKLKATWQEHFLRNICRNTIIFVDEPAMSA 183 GP+T+ +K GK IL+D+ L+ A T+ L LKA WQ +R R IIF DEP++S Sbjct: 130 GPITFATIVKGADGKAILFDQELTQAVTQGLALKAAWQAAKIRETGRWAIIFFDEPSLSG 189 Query: 184 YGSAYLPLSREQVTGMFDEVFSGI--SGL--KGVHCCGNTDWSILMDTRVDIINFDTYAY 239 +GSA++P+SRE+V + E + +GL G+HCCGNTDWS+L++T VDI++FD+Y Y Sbjct: 190 FGSAFMPISREEVIRLLTETITSARQAGLIYCGIHCCGNTDWSMLLETPVDILSFDSYEY 249 Query: 240 ANSLSIYTDEVKAFIKRGGAVAWGIVPTDEKALKEETAASLKDRLEAAMSHFDSHGLPFA 299 +L +Y +K F+ RGG +AWG+VPT A ET A+L R E+ + G+ Sbjct: 250 FGTLKLYAKVLKDFLARGGYLAWGLVPTSPTA-PIETEAALWQRFESQIRELADLGMDER 308 Query: 300 ELARHSLITPACGLGLKSPEAAERAPQLLAELS 332 + SL+TPACGLG SPE A A LA LS Sbjct: 309 LVLSQSLLTPACGLGYLSPEQARTAIVTLASLS 341 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: 316 Number of extensions: 16 Number of successful extensions: 5 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: 351 Length adjustment: 29 Effective length of query: 313 Effective length of database: 322 Effective search space: 100786 Effective search space used: 100786 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