Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate BPHYT_RS28730 BPHYT_RS28730 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__BFirm:BPHYT_RS28730 Length = 503 Score = 204 bits (519), Expect = 5e-57 Identities = 144/410 (35%), Positives = 212/410 (51%), Gaps = 32/410 (7%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFRE---PLDAFDDPSAEREPPVH 65 T +G +R DGR RN + + V C+ VAR I FR P + + P+ + + Sbjct: 101 TFQGIVRADGRVATRNYIGILTSVNCSATVARAIADHFRRDIHPEELAEFPNVDGV--IA 158 Query: 66 LIGFPGCY--PNGYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLVDV--VRASG 117 L GC G +L+R HPN +VL V LGCE+ L++ +R Sbjct: 159 LTHGSGCAIDSEGDGLAILQRTIGGYACHPNFASVLVVGLGCETNQIPRLLETQGLREHD 218 Query: 118 RPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGI 177 R + TIQ+ GGT STI G++ +R + ++ ++ S L +G CGGSDG SGI Sbjct: 219 R-LRTFTIQDSGGTTSTIAKGIELVRRMLPEANDVRREAVSASHLTVGLQCGGSDGYSGI 277 Query: 178 TANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALG----DEIVACVAKAA 233 TANP +G A D L+ G T I ET E+ G E + RAA P +G D I A A Sbjct: 278 TANPVLGAAVDLLVRHGGTAILSETPEIYGAEHLLTRRAATPEVGRKLLDRIRWWEAYAN 337 Query: 234 RYYSILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVV 293 R+ + + + A GN GGLTT EKSLG AK+G++ + + + GL +D Sbjct: 338 RHGAQMNNNPSA-GNKAGGLTTVLEKSLGGIAKAGSTNLTEVYEYAQPVTARGLVFMDTP 396 Query: 294 PDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLS 353 G+ +S + +A GA++I FTTGRGS G A +P +K+ N A ++ S Sbjct: 397 -------GYDPVSATGQ----VAGGANLICFTTGRGSAYGCAPTPSVKLATNTALWQRQS 445 Query: 354 GDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 DMD++ G +LEGR T++++G +FE + V+ G ++SE G EF+ Sbjct: 446 DDMDLNCGEVLEGRTTIEQLGGVLFELLLEVASGNRTRSEQHGYGQNEFV 495 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: 611 Number of extensions: 34 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: 503 Length adjustment: 33 Effective length of query: 398 Effective length of database: 470 Effective search space: 187060 Effective search space used: 187060 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