Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_050464920.1 AKL27_RS21520 altronate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_001189915.1:WP_050464920.1 Length = 511 Score = 203 bits (517), Expect = 9e-57 Identities = 142/410 (34%), Positives = 197/410 (48%), Gaps = 32/410 (7%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPP----- 63 T G +R DGR RN + V V C+ AR I FR + P A + P Sbjct: 109 TFMGIVRPDGRVATRNYIGVLTSVNCSATAARAIADYFRRDIH----PEALADFPNVDGV 164 Query: 64 VHLIGFPGCYPNGYAEKM------LERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASG 117 V L GC + E + L HPN AVL V LGCE+ L++ Sbjct: 165 VALTHGLGCAVDSLGEPLQILRRTLAGYARHPNFAAVLLVGLGCETNQISGLLEAHNLKE 224 Query: 118 RPV-EVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSG 176 TIQ GGT T+ G++ I+ ++ P+ L +G CGGSDG SG Sbjct: 225 NEYFHTFTIQSTGGTAKTVALGIEKIKKMLPAANNIKREPVPAKHLTLGLQCGGSDGYSG 284 Query: 177 ITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYY 236 ITANPA+G A D L+ G T I ET E+ G E + RA P +G++++A +A Y Sbjct: 285 ITANPALGAAVDLLVRHGGTAILSETPEIYGAEHLLTRRAVSPEVGEKLLARIAWWEEYC 344 Query: 237 SILG---HGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVV 293 + G + + + GN GGLTT EKSLGA AK G S +V + K + G +D Sbjct: 345 AKNGAEMNNNPSAGNKAGGLTTILEKSLGAVAKGGTSNLVDVYKYAETVTAKGFVFMDTP 404 Query: 294 PDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLS 353 G+ IS + +A GA+VI FTTGRGS G A SP +K+ N A ++ Sbjct: 405 -------GYDPISATGQ----VAGGANVICFTTGRGSAYGCAPSPSLKLATNTALWQRQE 453 Query: 354 GDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSET--LGHQEFI 401 DMD++ G I +G T ++G + F+ + + G +KSE G EF+ Sbjct: 454 EDMDINCGEIADGTATPQDIGAQFFQMILDTASGKKTKSELHGYGQDEFV 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: 625 Number of extensions: 42 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