Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate BPHYT_RS04770 BPHYT_RS04770 short-chain dehydrogenase
Query= uniprot:D8IS13 (254 letters) >FitnessBrowser__BFirm:BPHYT_RS04770 Length = 246 Score = 127 bits (319), Expect = 2e-34 Identities = 87/257 (33%), Positives = 137/257 (53%), Gaps = 27/257 (10%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKPHLDELAG---IAGVET--HLL 61 RL GK ++T A QGIG A+ FA+EGARV D++ + + AG + L Sbjct: 2 RLNGKVTIVTGAGQGIGAATALKFAKEGARVAVCDVNHDAVSRVVAACHAAGAQALGFTL 61 Query: 62 DVTDDAAIKALVA----KIGTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTI 117 DVT+ AA+ +VA + IDVL N AG + + + +D ++N + +FH Sbjct: 62 DVTNRAAVDGMVADVRERFRQIDVLVNNAGITRDARLQKMTLQQFDDVIDVNLRGVFHAA 121 Query: 118 RAVLPGMLAKKAGSIVNIASAASSVKGVANRFA---YGASKAAVVGLTKSVAADFVAQGI 174 +AV+ M+A+ +G I+N ASSV G+ + Y A+K V+G TK+ + + +GI Sbjct: 122 QAVVDTMIAQGSGVILN----ASSVVGLYGNYGQTNYAAAKFGVIGFTKTWSRELGPKGI 177 Query: 175 RCNAICPGTIESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLA 234 R NAI PG I++P L+ +EV A + P+ R+G EE+A + +LA Sbjct: 178 RVNAIAPGFIDTPILS-----------TVPQEVLAKMREQVPLRRLGTPEEIANIYAFLA 226 Query: 235 SDESNFTTGSIHMIDGG 251 SDE+++ G++ GG Sbjct: 227 SDEASYINGAVIEASGG 243 Lambda K H 0.317 0.130 0.365 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: 141 Number of extensions: 9 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: 254 Length of database: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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: 46 (22.3 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