Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate AO356_24195 AO356_24195 galactonate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24195 Length = 508 Score = 189 bits (481), Expect = 1e-52 Identities = 132/406 (32%), Positives = 200/406 (49%), Gaps = 28/406 (6%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPPVHLI 67 T EGY+R DGR G RN + V V C+ V ++I F E L F + V + Sbjct: 110 TFEGYVREDGRVGTRNYIGVISSVNCSATVCKQIANTFSAERLKDFPNVDGV----VAIT 165 Query: 68 GFPGCYPNGYAE------KMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVE 121 GC E + L H N VL + LGCE L++ + ++ Sbjct: 166 HGSGCGMGAQGEGIDILKRTLRGYADHANFAGVLLIGLGCEVNQLTPLMNELGDRSAALK 225 Query: 122 V-LTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITAN 180 L IQ++GGTR ++ G+ I + Q+ +A S L +G CGGSDG SGITAN Sbjct: 226 ASLVIQDEGGTREAVRRGIAHIEAMLPLVDQCQRTTVAASHLCVGLQCGGSDGYSGITAN 285 Query: 181 PAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV---AKAARYYS 237 PA+G A D L+ G T I ET E+ G E + RAA + +++A + R+ Sbjct: 286 PALGAAVDLLVQQGGTAILSETPEIYGAEHLLTARAASADIAAKLMARIHWWEAYVRHND 345 Query: 238 ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGE 297 + + + GN GG+TT EKSLGA AK+GA+ ++G+ + + GL +D Sbjct: 346 GDMNNNPSPGNKAGGITTILEKSLGAVAKAGATGLMGVYQYAETVDARGLVFMDTP---- 401 Query: 298 PRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMD 357 G+ +S + +A GA++I FTTGRGS G +P +K+ N ++ + DMD Sbjct: 402 ---GYDPVSATGQ----VAGGANLICFTTGRGSTYGCKPTPSLKIATNTRLFQRMELDMD 454 Query: 358 VDAGRILEGRGTLDEVGREVFEQTVAVSRG--AASKSETLGHQEFI 401 +AG I++G ++ + G +F +A + G S+ LG EF+ Sbjct: 455 FNAGGIVDGVESVAQAGERLFRLMLATASGHRTCSEENGLGDNEFL 500 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: 578 Number of extensions: 32 Number of successful extensions: 5 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: 508 Length adjustment: 33 Effective length of query: 398 Effective length of database: 475 Effective search space: 189050 Effective search space used: 189050 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 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