Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 16369 b2262 naphthoate synthase (NCBI)
Query= reanno::Pedo557:CA265_RS09125 (258 letters) >FitnessBrowser__Keio:16369 Length = 285 Score = 83.6 bits (205), Expect = 4e-21 Identities = 61/193 (31%), Positives = 99/193 (51%), Gaps = 7/193 (3%) Query: 2 ENLVLYQVAERIATITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGD-AF 60 E++ + + IA ITINRP+ +NA P + E+ A A DD + V+IL GD AF Sbjct: 23 EDIRYEKSTDGIAKITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIILTGAGDKAF 82 Query: 61 SAGADLAYLQQLQYNTFEENVADSNHLKKL--FTTIYYLPKVVIAQVEGHAIAGGCGLAT 118 +G D + Y ++++ + +HL L I PK V+A V G++I GG L Sbjct: 83 CSGGDQKV--RGDYGGYKDD-SGVHHLNVLDFQRQIRTCPKPVVAMVAGYSIGGGHVLHM 139 Query: 119 ICDIVFATPESNFGYTEVKIG-FVPAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYN 177 +CD+ A + FG T K+G F + ++ V + A+EI + + A++AL Sbjct: 140 MCDLTIAADNAIFGQTGPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAKQALDMG 199 Query: 178 LINFVTNSSDIHQ 190 L+N V +D+ + Sbjct: 200 LVNTVVPLADLEK 212 Lambda K H 0.318 0.133 0.367 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: 119 Number of extensions: 6 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: 258 Length of database: 285 Length adjustment: 25 Effective length of query: 233 Effective length of database: 260 Effective search space: 60580 Effective search space used: 60580 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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