Align [corrinoid iron-sulfur protein]-dependent methionine synthase (characterized)
to candidate WP_075858214.1 cpu_RS01415 methionine synthase
Query= metacyc::MONOMER-21502 (342 letters) >NCBI__GCF_001950255.1:WP_075858214.1 Length = 346 Score = 173 bits (438), Expect = 7e-48 Identities = 113/337 (33%), Positives = 173/337 (51%), Gaps = 18/337 (5%) Query: 9 LPTMIGSMPHTDPKAAVDIITHYLQDIPVWPQLPRRSCLEGMSAQFSQGLPGVKINQ--- 65 L T IGSMP D K ++II L IP WPQ+P+R E QF + L V + Q Sbjct: 5 LKTGIGSMPLVDVKKNLEIIKKALPQIPHWPQMPQRGIAEHFVFQFLRPLTEVGLLQVEG 64 Query: 66 DKVWIEPNPSFESELESLYQAYLD----NDFNKFPIGAEYAAGLYELASRN----LSPLL 117 +K + + +F +L Y+ Y + D+ F + E GLY L + + L Sbjct: 65 NKGIFKKDETFPEKLTFFYEKYFEALEKRDYAFFAMPRESGEGLYYLVEKFNESFSAALA 124 Query: 118 VKGHITGPLTYCMSIKDPSGKDILYDEVLSDAATKLLKLKATWQEHFLRNICRNTIIFVD 177 VKG + GPL+ +++ D + YD + +A K L + A WQ +FL+ R +FVD Sbjct: 125 VKGQMAGPLSILLTLTDENKIPAFYDPEIREAVVKTLVMSARWQVNFLKTTGRMVYLFVD 184 Query: 178 EPAMSAYGS-AYLPLSREQVTGMFDEVFSGI---SGLKGVHCCGNTDWSILMDTRVDIIN 233 +PA++ YGS +L L RE+V G+ E+ + I G+ GVH C DWSI+ + +I+ Sbjct: 185 DPAIANYGSFTHLTLKREEVVGVLKEIIAAILEEGGVPGVHSCAGIDWSIVTEAGAKVIS 244 Query: 234 FDTYAYANSLSIYTDEVKAFIKRGGAVAWGIVPTDEKALKEETAASLKDRLEAAMSHFDS 293 D Y +SL Y +EVK+ + GG +A GI+PT + ++ + L E ++ Sbjct: 245 VDAANYLDSLFPYKEEVKSLLSAGGILALGIIPTGPE-IENYSLEDLYADFEKKVNLLRE 303 Query: 294 HGLPFAELARHSLITPACGLGLKSPEAAERAPQLLAE 330 G+ + ++TPACG GL PE AE+ LL + Sbjct: 304 MGVVTND--SMLMLTPACGTGLLPPEQAEKIYSLLRD 338 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: 290 Number of extensions: 17 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: 346 Length adjustment: 29 Effective length of query: 313 Effective length of database: 317 Effective search space: 99221 Effective search space used: 99221 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 Jul 25 2024. The underlying query database was built on Jul 25 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