Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate Ac3H11_3953 D-galactarate dehydratase (EC 4.2.1.42)
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3953 Length = 525 Score = 159 bits (403), Expect = 1e-43 Identities = 128/406 (31%), Positives = 188/406 (46%), Gaps = 47/406 (11%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67 T EGY DG G RN++A+ V+C V V + ++ L P V +I Sbjct: 116 TFEGYRNADGSVGTRNILAITTTVQCVAGVVANAVRRIKDEL-------LPLYPQVDDVI 168 Query: 68 GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLVDVVR--- 114 G Y G A + L ++ +PN G V+ VSLGCE + L+ Sbjct: 169 GLEHTYGCGVAIDAPDAIIPIRTLRNISLNPNFGGEVMVVSLGCEKLQPDRLLPAGSFPI 228 Query: 115 ------ASGRPVEVLTIQEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTIC 168 A G L E G S + + V R E+L A+++ + SELV+G C Sbjct: 229 ADERDAALGPETVCLQADEHVGFMSMLDHIVQSARPHLERLNARRRETIRASELVLGVQC 288 Query: 169 GGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVAC 228 GGSD SG+TANPAVG D L+ AGAT +F E E+ + +RAA P + + IV Sbjct: 289 GGSDAFSGVTANPAVGFCADLLVRAGATVMFSENTEVRDAVEQLTSRAATPEVAESIVRE 348 Query: 229 VAKAARYYS---ILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDI---P 282 + RY + + GN GGL+ EK++G+ KSG +PI ++ PG+ Sbjct: 349 LGWYDRYLDRGRVDRAANTTPGNKAGGLSNIAEKAMGSIIKSGTAPISHVLAPGEKLRRD 408 Query: 283 PTGGLYLLDVVPDGEPRFGFPNISDNAEIGEL-IACGAHVILFTTGRGSVVGSAISPVIK 341 G +Y D G L +A G ++ +FTTGRG+ G A PV+K Sbjct: 409 QRGLVYAATPASD-------------FICGTLQLAAGMNLHVFTTGRGTPYGLAECPVVK 455 Query: 342 VCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 V R MD++AG+I +G +++E+G E+F + V+ G Sbjct: 456 VATRTDLARRWHDLMDINAGKIADGEASIEELGWEMFHLLLDVASG 501 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: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 431 Length of database: 525 Length adjustment: 33 Effective length of query: 398 Effective length of database: 492 Effective search space: 195816 Effective search space used: 195816 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