Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_038216213.1 Q392_RS27400 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000745855.1:WP_038216213.1 Length = 508 Score = 206 bits (525), Expect = 1e-57 Identities = 142/414 (34%), Positives = 208/414 (50%), Gaps = 26/414 (6%) Query: 2 PVAAQQPTLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQF-REPLDAFDDPSAER 60 P A ++ + G R DGR RN + V V C+ AR I F R A P Sbjct: 99 PPARREASFMGIRRADGRVATRNYIGVLTSVNCSATAARAIADHFSRRTNPAALAPYPHV 158 Query: 61 EPPVHLIGFPGCYPN--GYAEKMLERL----TTHPNVGAVLFVSLGCESMNKH-YLVDVV 113 + V L GC + G ++LER TH N VL V LGCE+ + +L Sbjct: 159 DGVVALTHGTGCGMDTQGLGMQILERTLTGYATHANFAGVLVVGLGCEANQINAWLATGH 218 Query: 114 RASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDG 173 + G + +IQ+ GGT T+Q G+ I + A ++ P + + + IG CGGSDG Sbjct: 219 LSEGENLRTFSIQDTGGTHKTVQKGIALIEEMLPRANAAKREPCSAAHITIGLQCGGSDG 278 Query: 174 TSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAA 233 SGI+ANPA+G A D L+ G T I ET E+ G E + RA R +G+++V + Sbjct: 279 YSGISANPALGAAVDLLVAHGGTAILSETPEIYGAEHLLTRRAVRREVGEKLVERI-HWW 337 Query: 234 RYYSILGHGSF----AVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYL 289 +Y+ + G + GN GGLTT EKSLGA AK G S + + + + G Sbjct: 338 EHYTAVNEGEMNNNPSPGNKAGGLTTILEKSLGAVAKGGTSNLEAVYEYAEPVAAHGFVY 397 Query: 290 LDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATY 349 +D G+ +S + +A GA++I FTTGRGS G A SP +K+ N A + Sbjct: 398 MDTP-------GYDPVSATGQ----VAGGANMICFTTGRGSAYGCAPSPSLKLATNSALW 446 Query: 350 RNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 + DMD++ G I++G T++++G+ +FE +A + G SKSE G EF+ Sbjct: 447 QRQEEDMDINCGEIIDGTATIEQMGQRIFELVLATASGQHSKSELHGYGQSEFV 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: 627 Number of extensions: 41 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 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