Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate 206645 DVU1206 3-oxoacyl-(acyl-carrier-protein) reductase (TIGR)
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__DvH:206645 Length = 259 Score = 91.7 bits (226), Expect = 1e-23 Identities = 76/246 (30%), Positives = 115/246 (46%), Gaps = 19/246 (7%) Query: 23 VITGGGSGIGAALVEAFVGQGAQVCFLDIATEP--SEALVASLKDAAVAPRFFPCNLMNL 80 ++TGG GIG A+ E G QV FL ++P +EA+ A ++DA + F ++ + Sbjct: 21 IVTGGSRGIGKAVAETLARAGLQV-FLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSDA 79 Query: 81 EALRATFTEIETVMGGVDILINNAANDD-----RHKSEDVTPAYWDERLAVNLRHQFFCA 135 A+ A F +D+L+NNA R K ED ++ L VNL F C Sbjct: 80 AAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDED-----FERVLDVNLCGAFTCL 134 Query: 136 QAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNA 195 + M ++ G I+N S+ +G Y AKAG+ G+T A++ V VNA Sbjct: 135 REASKLMTRQRLGRIINITSVVGQMGNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNA 194 Query: 196 IIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVR--VDPHDVAALALFLSSDSGAKCTGRE 253 + PG I T L PEE K + +P+R D+A FL+S+ + TG+ Sbjct: 195 VAPGFIETDMTAGL---PEEVRKAY-VEAIPLRRLGSAQDIADAVAFLASERASYITGQV 250 Query: 254 YYVDAG 259 V+ G Sbjct: 251 LAVNGG 256 Lambda K H 0.322 0.137 0.417 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: 167 Number of extensions: 14 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: 263 Length of database: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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 (21.9 bits) S2: 47 (22.7 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