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 CCNA_00092 CCNA_00092 short chain dehydrogenase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Caulo:CCNA_00092 Length = 296 Score = 112 bits (280), Expect = 9e-30 Identities = 85/266 (31%), Positives = 128/266 (48%), Gaps = 23/266 (8%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTS 67 + G VAVITGG SG+GL T E V +GA V DL + G ++ + FA DVT+ Sbjct: 5 LNGKVAVITGGCSGIGLGTVELFVAEGACVVAADLQDEKGRMLEQRFPDQVRFARCDVTA 64 Query: 68 EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127 + D+ +ALA+ FG +D+ N AG + + + F ++ MG + Sbjct: 65 DDDLAKTMALAESSFGGLDILFNNAGHGGTPASVPELTAEAWD-KTFALLVRGPAMGMTH 123 Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 + L+ G G IINTAS+A + G AYS++K ++ M+ A +L+ Sbjct: 124 ALPLMQKRGG----------GSIINTASIAGLQAGFGPLAYSSAKAAVIHMSRCAAAELS 173 Query: 188 PIGIRVMTIAPGLFGTPLL---TSLPEKVCNFLASQV--------PFP-SRLGDPAEYAH 235 P IRV I PGL T + LP +V + +A+Q+ P P S L + A Sbjct: 174 PQKIRVNAICPGLIATSIFGASMGLPREVADQMAAQIASIGPKIQPIPKSGLPEDIAAAA 233 Query: 236 LVQAIIENPFLNGEVIRLDGAIRMQP 261 L A ++ F+ G I +DG I + P Sbjct: 234 LYLASDDSRFVTGTHIVVDGGITVGP 259 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: 208 Number of extensions: 9 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: 296 Length adjustment: 25 Effective length of query: 236 Effective length of database: 271 Effective search space: 63956 Effective search space used: 63956 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