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_047214213.1 PATSB16_RS11230 glucose 1-dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_001931675.1:WP_047214213.1 Length = 255 Score = 96.7 bits (239), Expect = 4e-25 Identities = 81/255 (31%), Positives = 126/255 (49%), Gaps = 22/255 (8%) Query: 12 VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGE----AQAKKLGNNCVFAPADVTS 67 VA++TG A G+G A A RL +GA V+ D ++ AQ + G++ +V S Sbjct: 7 VALVTGSAQGIGRAIAVRLAQEGAKIVVEDRQDADAAEQTLAQVRAAGSDGCVIAGNVGS 66 Query: 68 EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127 D + + A K GR+DV VN AG+ + + + D+ VLDVNL G F Sbjct: 67 VHDARGVVDAAVAKLGRIDVLVNNAGVERNAPFLEVSEA------DYDLVLDVNLKGAFF 120 Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 + + V + + +GG+ I+N +SV +Y ASKGG+ M +A +LA Sbjct: 121 MTQAVVRHL--RDSHRGGR---IVNISSVHEELPFPHFTSYCASKGGMKMMVRNLAIELA 175 Query: 188 PIGIRVMTIAPGLFGTPLLTSL---PEKVCNFLASQVPFPSRLGDPAEYAH--LVQAIIE 242 P+GI V +APG GT + L P ++ LA+ +P RLG + A+ L A E Sbjct: 176 PLGITVNNVAPGAVGTAINNKLLHDPAELSALLAN-IPL-KRLGKVEDVANAVLFLASDE 233 Query: 243 NPFLNGEVIRLDGAI 257 ++ G + +DG + Sbjct: 234 ASYVTGTTVYVDGGL 248 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: 148 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 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