Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate BPHYT_RS16405 BPHYT_RS16405 galactonate dehydratase
Query= curated2:A8MA91 (398 letters) >FitnessBrowser__BFirm:BPHYT_RS16405 Length = 382 Score = 122 bits (307), Expect = 1e-32 Identities = 92/274 (33%), Positives = 145/274 (52%), Gaps = 23/274 (8%) Query: 68 VEVESSDGEVGFG---ISTGGYPAAWIIENHLSRFVVGKYVGEVEKTWDQMFKATIYYGR 124 +++E+ +G VG+G + + A +E LS +++GK +E W M+++ Y G Sbjct: 18 LKIETDEGIVGWGEPVVEGRAHTVAAAVEE-LSDYLIGKDPLLIEDHWQVMYRSGFYRGG 76 Query: 125 RGIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYA--TGPRP-DVA------ 175 I M+AI+ VD ALWD+ GK G+P++ LLGG VRD++ Y+ G RP DVA Sbjct: 77 P-ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWIGGDRPSDVANNARAV 135 Query: 176 -----KSLGFIGGKLPLIHGPADGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLPY 230 K++ G + I D ++G+ NV +EA VG + + D + P Sbjct: 136 VERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREA---VGPNIGIGVDFHGRVHKPM 192 Query: 231 AQRLLSELKPYGLFWIEEPFIPDDYWSFGALANIAPPTLVASGEHESTVHGFRLLLELGK 290 A+ L EL PY L +IEEP + ++ + + N T +A GE + F+ +L G Sbjct: 193 AKVLAKELDPYKLLFIEEPVLSENAEALRDIVN-QTNTPIALGERLYSRWDFKHILSGGY 251 Query: 291 VNVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPH 324 V++IQPD + GG+T KIA++AEAY + H Sbjct: 252 VDIIQPDASHAGGITECRKIASMAEAYDVALALH 285 Lambda K H 0.321 0.141 0.440 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: 426 Number of extensions: 22 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: 398 Length of database: 382 Length adjustment: 30 Effective length of query: 368 Effective length of database: 352 Effective search space: 129536 Effective search space used: 129536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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