Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate CA265_RS04670 CA265_RS04670 altronate hydrolase
Query= reanno::BFirm:BPHYT_RS34230 (431 letters) >FitnessBrowser__Pedo557:CA265_RS04670 Length = 545 Score = 138 bits (348), Expect = 4e-37 Identities = 98/330 (29%), Positives = 154/330 (46%), Gaps = 19/330 (5%) Query: 80 KMLERLTTHPNVGAVLFVSLGCESMN----KHYLVDVVRASGRPVEVLTIQEKGGTRSTI 135 K+L HPNV + +SLGC+ + K L + +P+ + Q+ I Sbjct: 219 KLLAAYAHHPNVAGITVLSLGCQHLQVEDFKRDLFALDPDFDKPLLIFEQQKAQSEEELI 278 Query: 136 QYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGRAFDHLIDAGA 195 Q + + Q + LS++ +G CGGSDG SGI+ANP+VG D L+ GA Sbjct: 279 QNSIRSTFEGLMFINKQARAAAPLSKMCVGVKCGGSDGFSGISANPSVGYCADLLVALGA 338 Query: 196 TCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHGSF---AVGNADGG 252 + E EL G E M R+ ++ + + + +G G + + GN G Sbjct: 339 KVLLAEFPELCGVEQEMIDRSVDQPTAEKFIRLMTEYDDLAHKVGSGFYMNPSPGNIKDG 398 Query: 253 LTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFGFPNISDNAEIG 312 L T KS GA K+G++PIV ++ + GL L+ P A G Sbjct: 399 LITDAIKSAGAARKAGSAPIVDVLDYTEPATKPGLSLVCT----------PGNDVEATTG 448 Query: 313 ELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAGRILEGRGTLDE 372 + A GA +ILFTTG G+ G+ + P IKV N + +S +D+D G ++ G T++E Sbjct: 449 KA-AAGATLILFTTGLGTPTGNPVCPTIKVATNSILAKRMSDIIDIDTGAVINGEKTINE 507 Query: 373 VGREVFEQTVAVSRG-AASKSETLGHQEFI 401 +G ++ E + V+ G K+ L +FI Sbjct: 508 MGEDILEYCIKVASGEEIPKAVQLNQDDFI 537 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: 592 Number of extensions: 36 Number of successful extensions: 4 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: 545 Length adjustment: 34 Effective length of query: 397 Effective length of database: 511 Effective search space: 202867 Effective search space used: 202867 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: 52 (24.6 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