Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate Echvi_3632 Echvi_3632 Altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Cola:Echvi_3632 Length = 548 Score = 146 bits (369), Expect = 1e-39 Identities = 101/322 (31%), Positives = 155/322 (48%), Gaps = 19/322 (5%) Query: 88 HPNVGAVLFVSLGCESMNKHYL---VDVVRAS-GRPVEVLTIQEKGGTRSTIQYGVDWIR 143 +PNV +SLGC++ L +D + +PV +L Q++G + + + Sbjct: 230 NPNVAGATILSLGCQNAQPSILREKLDKINPDLKKPVIILEQQQEGTENTLLTNAIQKTF 289 Query: 144 GAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETG 203 A ++ P LS+L +G CGGSDG SGI+ANP+VG A D ++ G I E Sbjct: 290 LALTDADQLERQPAPLSKLTVGLECGGSDGFSGISANPSVGHASDLVVALGGKTILSEFP 349 Query: 204 ELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG---SFAVGNADGGLTTQEEKS 260 EL G E + R D+ V + A +G G + + GN GL T KS Sbjct: 350 ELCGVEQELINRCTTDESADKFVTLMRAYAASAEAVGSGFDMNPSPGNIKDGLITDAMKS 409 Query: 261 LGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAH 320 GA K G SPIV ++ + GL LL P +D + GA+ Sbjct: 410 AGAAKKGGTSPIVDVLDYAEYVTKPGLNLL-CTPG----------NDVESTTAMAGSGAN 458 Query: 321 VILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQ 380 VILFTTG G+ G+ ++PV+KV +N + +D++ G ++ G T+D++G E+ E Sbjct: 459 VILFTTGLGTPTGNPVTPVLKVSSNHILAEKMDDIIDINTGGVISGDKTIDQMGEEILEH 518 Query: 381 TVAVSRG-AASKSETLGHQEFI 401 + V+ G +K+ TL +FI Sbjct: 519 IIEVASGNKKAKAMTLNQDDFI 540 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: 576 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 431 Length of database: 548 Length adjustment: 34 Effective length of query: 397 Effective length of database: 514 Effective search space: 204058 Effective search space used: 204058 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: 52 (24.6 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