Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 3608645 Dshi_2038 Altronate dehydratase (RefSeq)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Dino:3608645 Length = 393 Score = 161 bits (408), Expect = 3e-44 Identities = 130/411 (31%), Positives = 196/411 (47%), Gaps = 48/411 (11%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPL---DAFDDPSAEREPPVH 65 T++GY R +GR G+RN V + + + ++ + + L A+ + +H Sbjct: 9 TVKGYRRENGRVGVRNHVLILPVDDISNAACEAVANNVKGTLAIPHAYGRLQFGEDLELH 68 Query: 66 LIGFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTI 125 G N PNV +V V +G E + D +R +G+ V +I Sbjct: 69 FRTMIGTGAN-------------PNVHSV--VVIGIEPGWTKRIADGIRETGKEVAEFSI 113 Query: 126 QEKGG---TRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPA 182 ++KG R+ D++ A E Q+ ++SEL + T CG SD T+G+ + P Sbjct: 114 EQKGDFETIRAASWAAKDFVHKATEM----QREECSISELWVSTKCGESDTTTGLGSCPT 169 Query: 183 VGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG 242 VG +D L+ G T F ET E+ G E + RA +G + KA + I H Sbjct: 170 VGNMYDKLLPEGITGFFGETSEITGAEHICQKRAINEEVGQRWYK-MWKAYQDDVIFAHQ 228 Query: 243 SFAV-------GNADGGLTTQEEKSLGAYAKSG-ASPIVGIIKPGDIPPTG-GLYLLDVV 293 + + GN +GGLTT EEK+LG K G S + I++P + P +G GLY +D Sbjct: 229 TDDLSDSQPTKGNIEGGLTTIEEKALGNLEKIGRTSQFIDILEPAEQPKSGNGLYFMD-- 286 Query: 294 PDGEPRFGFPNISDNAEIGELIACGAHVI-LFTTGRGSVVGSAISPVIKVCANPATYRNL 352 + S AE L+A G VI F TG+G+VVG+ I PVIK+ ANP T R + Sbjct: 287 ----------SSSAAAECVTLMAAGGAVIHTFPTGQGNVVGNPIVPVIKITANPRTVRTM 336 Query: 353 SGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILT 403 + +DVD IL T+DE G + E + G + +E LGH+EF +T Sbjct: 337 AEHVDVDVSGILRREMTIDEAGDALIEMICRTANGRNTAAEALGHREFSMT 387 Lambda K H 0.318 0.137 0.408 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: 432 Number of extensions: 25 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: 431 Length of database: 393 Length adjustment: 31 Effective length of query: 400 Effective length of database: 362 Effective search space: 144800 Effective search space used: 144800 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: 50 (23.9 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