Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_012405572.1 BPHY_RS31760 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >NCBI__GCF_000020045.1:WP_012405572.1 Length = 530 Score = 158 bits (399), Expect = 4e-43 Identities = 129/415 (31%), Positives = 196/415 (47%), Gaps = 55/415 (13%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIG 68 T EGY DG G RN++A+ V+C V + VT+ + L P+ V +G Sbjct: 111 TFEGYRNADGSVGTRNILAITTTVQCVADVVQHAVTRIKSELL----PNYPNVDDVVSLG 166 Query: 69 FP-GC-----YPNGYAE-KMLERLTTHPNVGA-VLFVSLGCESM---------------- 104 GC P+ + + ++ +PN G V+ VSLGCE + Sbjct: 167 HTYGCGVAIDAPDAMVPIRTVRNISLNPNFGGEVMMVSLGCEKLQPERLMPPGTIPIATA 226 Query: 105 -NKHYLVDVVRASGRPV--EVLTIQEKG--GTRSTIQYGVDWIRGAREQLAAQQKVPMAL 159 N + D+ S + EV+T+Q+ G ++ I+ + G ++L A+++ Sbjct: 227 TNTEDVADIGDLSAKTANGEVVTLQDDSHVGFQAMIESIMKMAEGHLKRLDARRRETCPA 286 Query: 160 SELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARP 219 S+LV+G CGGSD SG+TANPAVG A D L+ AGAT +F E E+ + RAA Sbjct: 287 SDLVVGVQCGGSDAFSGLTANPAVGFATDLLVRAGATVLFSEVTEVRDGVGQLTARAANA 346 Query: 220 ALGDEIVACVAKAARYY-SILGHG------SFAVGNADGGLTTQEEKSLGAYAKSGASPI 272 ++ A + + +Y S L G + GN GGL+ EK++G+ KSG SPI Sbjct: 347 ----QVAAAIIREMEWYDSYLKRGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSPI 402 Query: 273 VGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVV 332 G++ PG+ GL + SD +A G ++ +FTTGRG+ Sbjct: 403 SGVLSPGEKATQKGLI-----------YAATPASDFICGTLQVAAGINLHVFTTGRGTPY 451 Query: 333 GSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 G A PVIK+ R +DV+AG I G T+++VG E+F + V+ G Sbjct: 452 GLAEVPVIKLATRSDLARRWYDLIDVNAGTIATGEATIEDVGWELFHLMLEVASG 506 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: 644 Number of extensions: 43 Number of successful extensions: 6 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: 530 Length adjustment: 34 Effective length of query: 397 Effective length of database: 496 Effective search space: 196912 Effective search space used: 196912 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