Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_012171801.1 AZC_RS16890 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000010525.1:WP_012171801.1 Length = 507 Score = 210 bits (534), Expect = 9e-59 Identities = 148/404 (36%), Positives = 205/404 (50%), Gaps = 24/404 (5%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP-VHLI 67 T EG+ R DGR G RN + + V C+ VA I + D P+ + P H Sbjct: 109 TFEGFRRADGRAGTRNYIGILSSVNCSATVADYIADEVTRSGILADYPNIDGVVPFTHGT 168 Query: 68 GFPGCYPNGYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLVDVVR-ASGRPVEV 122 G G G +L R THPN AVL + LGCE L + G + Sbjct: 169 GC-GMGSKGEEFDILARTQWGYATHPNFAAVLVIGLGCEVFQIPRLKEAYGIVEGEHFQS 227 Query: 123 LTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPA 182 LTIQE GGTR ++ GV ++ + ++ +A SEL++ CGGSDG SG+TANPA Sbjct: 228 LTIQESGGTRKSVAAGVARVKEMLAFANSSRRQTVAASELMLALQCGGSDGYSGLTANPA 287 Query: 183 VGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILG-- 240 +G A D L+ G T I ET E+ G E + RA A+G +IV + Y + G Sbjct: 288 LGAAVDILVRQGGTAILSETPEIFGAEHLLTRRAESEAVGRKIVDLIDWWTDYAARAGGE 347 Query: 241 -HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPR 299 + + + GN GGLTT EKSLGA AK G S + G+ + + G +D Sbjct: 348 LNNNPSPGNKAGGLTTILEKSLGAVAKGGTSTLRGVYRYAERIDRKGFVYMDT------- 400 Query: 300 FGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVD 359 P A G+ +A GA+V+ FTTGRGS G +P IK+ N YR + DMD++ Sbjct: 401 ---PGYDPVAATGQ-VAGGANVLCFTTGRGSAYGCKPTPSIKLATNSDLYRRMEEDMDLN 456 Query: 360 AGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGH--QEFI 401 G +LEG +++E GRE+F+ + V+ G SKSE LG+ EF+ Sbjct: 457 CGDVLEG-VSIEEKGREIFQTVLDVASGTRSKSELLGYGRNEFV 499 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: 587 Number of extensions: 34 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 431 Length of database: 507 Length adjustment: 33 Effective length of query: 398 Effective length of database: 474 Effective search space: 188652 Effective search space used: 188652 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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