Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_011801457.1 PNAP_RS10380 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000015505.1:WP_011801457.1 Length = 511 Score = 208 bits (529), Expect = 4e-58 Identities = 140/402 (34%), Positives = 212/402 (52%), Gaps = 24/402 (5%) Query: 11 EGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFR-EPLDAFDDPSAEREPPVHLIGF 69 +G++R DGR RN + V V C+ V R I FR + L F P+ + + Sbjct: 115 QGFVRQDGRVATRNYLGVISSVNCSATVCRHIADAFRGDALAGF--PNVDGVVAITHGSG 172 Query: 70 PGCYPNGYAEKMLERL----TTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPV-EVLT 124 G NG ++L+R HPN VL + LGCE LV ++A + LT Sbjct: 173 CGMGGNGEGLELLQRTLRGYANHPNFAGVLVIGLGCEVNQIAPLVQTLQARAPGMFATLT 232 Query: 125 IQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVG 184 IQ++GGTR TI G ++ + Q+ P+ LS LV+G CGGSDG SGI+ANPA+G Sbjct: 233 IQDEGGTRETIAQGKLLLQDMLQTANLAQREPVPLSHLVVGLQCGGSDGYSGISANPALG 292 Query: 185 RAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILG---H 241 A D L+ G T I ET E+ G E + RA PA+ D+++ + Y ++ G + Sbjct: 293 AAVDLLVRHGGTAILSETPEIYGAEHLLTHRAVSPAVADKLMHRLQWWEAYAALHGGDLN 352 Query: 242 GSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFG 301 + + GN GG+TT EKSLGA AK+G+S ++ +++ + GL +D G Sbjct: 353 NNPSPGNKAGGITTILEKSLGAVAKAGSSRLMDVLEYAEPVHAQGLVFMDTP-------G 405 Query: 302 FPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAG 361 + +S + +A GA++I FTTGRGS G +P +K+ N ++ + DMD D G Sbjct: 406 YDPVSATGQ----VAGGANLICFTTGRGSTYGCKPTPSLKLATNTPMFQRMQLDMDFDCG 461 Query: 362 RILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 I++G+ ++ E G +F + + GAA++SE LG EF+ Sbjct: 462 AIVDGQASIAETGEALFRLMLETASGAATRSEQNGLGDNEFL 503 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: 613 Number of extensions: 37 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: 511 Length adjustment: 33 Effective length of query: 398 Effective length of database: 478 Effective search space: 190244 Effective search space used: 190244 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