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 GFF1782 PS417_09065 short-chain dehydrogenase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__WCS417:GFF1782 Length = 253 Score = 102 bits (254), Expect = 8e-27 Identities = 82/261 (31%), Positives = 126/261 (48%), Gaps = 34/261 (13%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGE---AQAKKLGNNCVFAPADVT 66 G VA++TG A+G+G ATA +G V+ DL +GGE A + G +F +VT Sbjct: 7 GQVALVTGAAAGIGRATALAFAAEGLKVVVADLDATGGENTVALIHQAGGEALFVRCNVT 66 Query: 67 SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTH--TLEDFQRVLDVNLMG 124 E DVQ +A +GR+D A N AGI + +KG+ +L++F ++ VN+ G Sbjct: 67 LEADVQQLMAQTLAAYGRLDYAFNNAGIEI-------EKGKLADGSLDEFDAIMGVNVKG 119 Query: 125 TFNVIR-----LVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMT 179 + ++ L+A QGG G I+NTASVA + Y+ASK ++G+T Sbjct: 120 VWLCMKHQLPLLLA---------QGG--GAIVNTASVAGLGAAPKMSIYAASKHAVIGLT 168 Query: 180 LPIARDLAPIGIRVMTIAPGLFGTPLLTSLPE---KVCNFLASQVPFPSRLGDPAEYAHL 236 A + A IRV + P + T + E + F A+ P R+G E A Sbjct: 169 KSAAIEYAKKKIRVNAVCPAVIDTDMFRRAYEADPRKAEFAAAMHPV-GRIGKVEEIASA 227 Query: 237 VQAIIEN--PFLNGEVIRLDG 255 V + + F G+ + +DG Sbjct: 228 VLYLCSDGAAFTTGQALAVDG 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: 179 Number of extensions: 4 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: 261 Length of database: 253 Length adjustment: 24 Effective length of query: 237 Effective length of database: 229 Effective search space: 54273 Effective search space used: 54273 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 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