Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate H281DRAFT_05320 H281DRAFT_05320 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Burk376:H281DRAFT_05320 Length = 529 Score = 148 bits (374), Expect = 3e-40 Identities = 125/416 (30%), Positives = 185/416 (44%), Gaps = 58/416 (13%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67 T EGY DG G RN++A+ V+C V V + + L + P V ++ Sbjct: 111 TFEGYRNADGSVGSRNILAITTTVQCVADVVEHAVVRIKSEL-------LPKYPNVDDVV 163 Query: 68 GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLVDV----V 113 G Y G A + + + +PN G V+ VSLGCE + L+ + Sbjct: 164 GLGHTYGCGVAIDAPDAMVPIRTVRNIALNPNFGGEVMMVSLGCEKLQPERLMPPGTIPI 223 Query: 114 RASGRPVEVLTIQEKG----------------GTRSTIQYGVDWIRGAREQLAAQQKVPM 157 A+ P E+ I + G G +S ++ + G ++L +++ Sbjct: 224 AAAQNPSEIADIGDLGADENGDVVVLQDEAHVGFQSMVESIMRTAEGHLKRLNNRRRETC 283 Query: 158 ALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAA 217 ++LV+G CGGSD SG+TANPAVG A D L+ AGAT +F E E+ + RA Sbjct: 284 PAADLVVGVQCGGSDAFSGLTANPAVGFATDLLVRAGATVMFSEVTEVRDGVDQLTARAE 343 Query: 218 RPALGDEIVACVAKAARYYSILGHG------SFAVGNADGGLTTQEEKSLGAYAKSGASP 271 D A + + Y L G + GN GGL+ EK++G+ KSG SP Sbjct: 344 N---ADVAQAIIREMQWYDDYLKRGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSP 400 Query: 272 IVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSV 331 I G++ PG+ GL + SD +A G ++ +FTTGRG+ Sbjct: 401 ISGVLSPGEKVRQKGLI-----------YAATPASDFICGTLQLAAGINLHVFTTGRGTP 449 Query: 332 VGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 A PVIKV R MD++AG I G T++EVG E+F + V+ G Sbjct: 450 YSLAEVPVIKVATRSDLARRWHDLMDINAGTIATGSATIEEVGWELFRFMLDVASG 505 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: 649 Number of extensions: 49 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: 529 Length adjustment: 34 Effective length of query: 397 Effective length of database: 495 Effective search space: 196515 Effective search space used: 196515 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