Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate 18291 b4266 gluconate 5-dehydrogenase (NCBI)
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__Keio:18291 Length = 254 Score = 124 bits (312), Expect = 1e-33 Identities = 79/248 (31%), Positives = 114/248 (45%) Query: 16 SLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFPC 75 SLAGK ++ITG GIG L GAQ+ DI E +E V L + P Sbjct: 6 SLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQAVAAPF 65 Query: 76 NLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFCA 135 N+ + + A IE +G +D+L+NNA RH + W++ +AVN F + Sbjct: 66 NVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFTEFPEQEWNDVIAVNQTAVFLVS 125 Query: 136 QAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNA 195 QAV M ERK G ++N S+ LG +T Y +K ++ +T GM + R ++VN Sbjct: 126 QAVTRHMVERKAGKVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNG 185 Query: 196 IIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSSDSGAKCTGREYY 255 I PG +T L A + DP ++ A+FLSS + G + Sbjct: 186 IAPGYFKTEMTKALVEDEAFTAWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLF 245 Query: 256 VDAGWLGA 263 VD G L A Sbjct: 246 VDGGMLVA 253 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: 175 Number of extensions: 12 Number of successful extensions: 2 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: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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 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