Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate PP_2723 PP_2723 Uncharacterized oxidoreductase YhdF
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__Putida:PP_2723 Length = 285 Score = 98.6 bits (244), Expect = 1e-25 Identities = 77/247 (31%), Positives = 113/247 (45%), Gaps = 9/247 (3%) Query: 17 LAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIAT-EPSEALVASLKDAAVAPRFFPC 75 LAGK +ITG SGIG A+ A+ +GA V + + ++ +K A P Sbjct: 40 LAGKIALITGADSGIGRAVAIAYAREGADVAIAYLNEHDDAQETARWVKAAGRQCLLLPG 99 Query: 76 NLMNLEALRATFTEIETVMGGVDILINNAANDDRHKS-EDVTPAYWDERLAVNLRHQFFC 134 +L + + G +DIL+NNAA H+S +D+ W + N+ F Sbjct: 100 DLAQKQHCHDIVDKTVAQFGRIDILVNNAAFQMAHESLDDIDDDEWVKTFDTNITAIFRI 159 Query: 135 AQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVN 194 Q LP M KGG I+N S++ P L Y K I T G+A+ G+ G+RVN Sbjct: 160 CQRALPSMP--KGGSIINTSSVNSDDPSPSLLAYAATKGAIANFTAGLAQLLGKQGIRVN 217 Query: 195 AIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPV--RVDPHDVAALALFLSSDSGAKCTGR 252 ++ PG I TP L+ T +EA P+ P +VA + + L SD + +G Sbjct: 218 SVAPGPIWTP---LIPATMPDEAVRNFGSGYPMGRPGQPVEVAPIYVLLGSDEASYISGS 274 Query: 253 EYYVDAG 259 Y V G Sbjct: 275 RYAVTGG 281 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: 195 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: 285 Length adjustment: 25 Effective length of query: 238 Effective length of database: 260 Effective search space: 61880 Effective search space used: 61880 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