Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_068174146.1 HTA01S_RS17590 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_001592305.1:WP_068174146.1 Length = 265 Score = 124 bits (311), Expect = 2e-33 Identities = 93/254 (36%), Positives = 137/254 (53%), Gaps = 24/254 (9%) Query: 9 KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSE 68 +G V ++TGGA G+G A A R +GA+ V+ D+ + G+A A +L + ++ DV S Sbjct: 18 QGRVVIVTGGAQGIGEACARRFASEGANVVIADVDDPRGQALANQL--DALYVHCDVGSA 75 Query: 69 KDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNV 128 +V+ +A + GRVDV VN AGI A+ + T EDF VL VNL G F + Sbjct: 76 DEVKACVAQTLARHGRVDVLVNNAGIFKAADFLEV------TEEDFDAVLRVNLKGAFLM 129 Query: 129 IRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAP 188 + VA EM GG G I+N +SV A+Y+ SKGGI +T +A LA Sbjct: 130 GQAVAREMAAT----GG--GCIVNMSSVNGVLAIPNIASYNVSKGGINQLTRVMALALAE 183 Query: 189 IGIRVMTIAPGLFGTPL-----LTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN 243 GIRV +APG T L LTS ++ + + S+ P RLG+P+E A +V + + Sbjct: 184 RGIRVNAVAPGTIATELAARAVLTS--DEAKHKIMSRTPM-KRLGEPSEIADVVAWLASD 240 Query: 244 --PFLNGEVIRLDG 255 ++ GE++ +DG Sbjct: 241 AASYVTGEIVTVDG 254 Lambda K H 0.318 0.135 0.385 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: 193 Number of extensions: 18 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: 261 Length of database: 265 Length adjustment: 25 Effective length of query: 236 Effective length of database: 240 Effective search space: 56640 Effective search space used: 56640 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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