Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate Dsui_2089 Dsui_2089 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >FitnessBrowser__PS:Dsui_2089 Length = 251 Score = 120 bits (300), Expect = 4e-32 Identities = 84/260 (32%), Positives = 126/260 (48%), Gaps = 19/260 (7%) Query: 6 KVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGRRVI 65 K+ ++TGGSRG+GR A+ AA G D+ + Y R A VVA+IEALGRR + Sbjct: 3 KIALITGGSRGLGRNAALKLAARGVDIILTY-------RSRADEAAAVVAQIEALGRRAV 55 Query: 66 AI-------EGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTV 118 A+ G A E +Q + T + + D L +NAG+ AF + + + Sbjct: 56 ALPLAVDEAAGFPAFAEAVRQALAGTWQR-ERFDFLVNNAGMGINAAFAETTEAQFDLLM 114 Query: 119 AVNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCA 178 +L G F++TQA + L GG I+ S+ A Y K G+ L + A Sbjct: 115 NTHLKGPFFLTQAL---LPLLNDGGRILNVSTGLARFALPGYAAYASMKGGIEVLTRYLA 171 Query: 179 VALGPYGIRCNSVMPGTIATDLNAQDLADEAK-KAYFEKRIPLGRLGRPEDVADCVTFLA 237 LGP GI N + PG I TD + D A+ A+ + LGR+G+P+D+ V L Sbjct: 172 KELGPRGIAVNVLAPGAIETDFGGGAVRDNAQLNAFIAAQTALGRVGQPDDIGHAVAALL 231 Query: 238 SDRARYVTGAALLVDGGLFV 257 S+ ++T + GG+F+ Sbjct: 232 SEETGWITAQRIEASGGMFL 251 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: 159 Number of extensions: 11 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: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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