Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate Ga0059261_2843 Ga0059261_2843 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__Korea:Ga0059261_2843 Length = 263 Score = 127 bits (320), Expect = 2e-34 Identities = 88/254 (34%), Positives = 124/254 (48%), Gaps = 12/254 (4%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L+ KV +VT G+ GIG A+A A GAD+ + GD D G R V A IEA+GR Sbjct: 3 LQGKVAVVTAGANGIGEGAALALAGMGADIVL---GDIDAHNGAR-----VAAAIEAIGR 54 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNL 122 R ++ + + LV FG++D+L +NAG AFLD + +N Sbjct: 55 RAAFRPADMMQADQARALVDFAAAEFGRIDILVNNAGGVRPRAFLDQNEGNWQRVTDLNF 114 Query: 123 NGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVALG 182 TQ+AA+ M GGAIV +S AL + Y KA + ++ A+ L Sbjct: 115 TSMLAATQSAARVM---ANGGAIVNVASTEALRAAPGFSVYAACKAAMVEFTKTMALELA 171 Query: 183 PYGIRCNSVMPGTIAT-DLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 P IR N + P I T L D A+ A ++ +PLGR+ + + FLAS A Sbjct: 172 PRAIRVNCIAPDLIDTPGLRPHMPTDPARIAARDRHVPLGRMATIHEAGSVIAFLASPAA 231 Query: 242 RYVTGAALLVDGGL 255 +VTGA + VDGG+ Sbjct: 232 SWVTGATIPVDGGI 245 Lambda K H 0.319 0.134 0.386 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: 163 Number of extensions: 6 Number of successful extensions: 3 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: 260 Length of database: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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: 47 (22.7 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