Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate GFF376 Psest_0377 galactarate dehydratase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__psRCH2:GFF376 Length = 521 Score = 154 bits (389), Expect = 6e-42 Identities = 121/396 (30%), Positives = 186/396 (46%), Gaps = 35/396 (8%) Query: 9 TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67 T EG+ DG G RN++ ++ V+C V V + R+ L + P V ++ Sbjct: 120 TFEGFRNSDGTVGTRNILGISTTVQCVTGVLEHAVKRIRDEL-------LPKYPNVDDVV 172 Query: 68 GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLVDVVRASG 117 Y G A + + L +PN+G L +SLGCE + ++ S Sbjct: 173 ALTHSYGCGVAINARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAEQVMHEGDPSV 232 Query: 118 --RPVEVLTIQEKG-GTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGT 174 R + +QE G I+ + ++L +++ + SEL++G CGGSD Sbjct: 233 DLREPWLYRLQESNSGFGEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAF 292 Query: 175 SGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAAR 234 SGITANPA+G A D L+ AGAT +F E E+ + + RA P + D ++A + R Sbjct: 293 SGITANPALGYAADLLVRAGATVMFSENTEVRDAVYMLTARAETPEVADALIAEMDWYDR 352 Query: 235 YY---SILGHGSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLD 291 Y + + GN GGL+ EKSLG+ KSG+ I G++ PG GL Sbjct: 353 YLERGAADRSANTTPGNKKGGLSNIVEKSLGSIVKSGSGAISGVVGPGGRVARKGLI--- 409 Query: 292 VVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRN 351 F SD +A G ++ +FTTGRG+ G A++PV+KV Sbjct: 410 --------FCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVATRTELAER 461 Query: 352 LSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRG 387 +D+DAGRI GR +++E+G E+F + V+ G Sbjct: 462 WPDLIDIDAGRIASGRASIEELGWELFHYYLDVASG 497 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: 620 Number of extensions: 34 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: 521 Length adjustment: 33 Effective length of query: 398 Effective length of database: 488 Effective search space: 194224 Effective search space used: 194224 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