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_057508628.1 ABB28_RS10765 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_001431535.1:WP_057508628.1 Length = 252 Score = 122 bits (307), Expect = 6e-33 Identities = 90/258 (34%), Positives = 124/258 (48%), Gaps = 16/258 (6%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKL---GNNCVFAPAD 64 +KG A++TGG SG+GLA AE L GA+ + DL +A + L G + D Sbjct: 6 LKGKTAIVTGGVSGIGLAVAEMLAASGAAISVWDLKQEAVDATTEALRGKGVKAIGIALD 65 Query: 65 VTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124 VT E V+ A+A + G VD+AVN AGIA + + ++ +++V+DVNL Sbjct: 66 VTDEAAVEAAVARTVAELGSVDIAVNNAGIAGPAAISG-----DYPVDGWRKVIDVNLTS 120 Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184 F R M G G IIN AS+ G G AY+A+K G+VG+T A Sbjct: 121 VFLCQRAQIQAMRD-----AGNGGSIINMASILGQVGYAGSVAYAAAKHGVVGLTQTAAW 175 Query: 185 DLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN- 243 + A IR+ + PG TPLL + KV L S+ RLG P E A LV + + Sbjct: 176 EHASDQIRINAVGPGFISTPLLEQMDPKVRATLESRHAL-KRLGTPEEVAALVAWLASDA 234 Query: 244 -PFLNGEVIRLDGAIRMQ 260 F G +DG Q Sbjct: 235 ASFATGTYYAIDGGYLAQ 252 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: 144 Number of extensions: 8 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: 261 Length of database: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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