Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate GFF2105 Psest_2148 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__psRCH2:GFF2105 Length = 285 Score = 145 bits (365), Expect = 1e-39 Identities = 93/257 (36%), Positives = 137/257 (53%), Gaps = 12/257 (4%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L+ K I+TGG GIGR++AV A EGADVAI Y + + R+ V E GR Sbjct: 39 LEGKTAIITGGDSGIGRSVAVLFAREGADVAILYLDQHQDAEETRTVV-------EQYGR 91 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAG-ICPFHAFLDMPPEVLESTVAVN 121 R + G+VA R+ ++++ T+ AFGK+D+L +NA P D+ E E T N Sbjct: 92 RCLTFAGDVADRDVCRKVIDETLAAFGKLDILVNNAAEQHPQEKLEDISEEQWEKTFRTN 151 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181 + G F +T+A + G G +I+ T+S++A G Y+ TK + + +S ++ L Sbjct: 152 IFGMFQMTKAVLPHL---GKGASIINTTSVTAYKGSPQLLDYSATKGAITAFTRSLSMNL 208 Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241 GIR N V PG I T L + D + A F P+ R G+P++VA +LAS A Sbjct: 209 AERGIRVNGVAPGPIWTPLISSTF-DADEVAEFGSNTPMKRPGQPDEVAPAYVYLASSDA 267 Query: 242 RYVTGAALLVDGGLFVN 258 YV+G + V+GG VN Sbjct: 268 AYVSGQVIHVNGGTVVN 284 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: 154 Number of extensions: 10 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: 260 Length of database: 285 Length adjustment: 25 Effective length of query: 235 Effective length of database: 260 Effective search space: 61100 Effective search space used: 61100 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