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 3608022 Dshi_1429 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Dino:3608022 Length = 256 Score = 115 bits (287), Expect = 1e-30 Identities = 86/258 (33%), Positives = 128/258 (49%), Gaps = 21/258 (8%) Query: 6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADV 65 R + G A++TG ASG G A R V +GA ++DL G +A A L N + DV Sbjct: 8 RRLSGKTAIVTGAASGFGREIARRFVREGARVAIVDLNGEGAKAVADALQQNAIAVTCDV 67 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 + DV A+ FGRVD+A+N AG ++ + E F+RV +VN+ Sbjct: 68 SKGADVSRAVQETIDAFGRVDIAINNAG-----WSHRNQPALDVDFETFKRVYEVNVDSI 122 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185 F+ + + D GG GV+IN S A + G + Y++SKG + MT +A + Sbjct: 123 FHATHALV----PHWRDIGG--GVMINVGSTAGIRPRPGLSWYNSSKGAVNMMTKTLAVE 176 Query: 186 LAPIGIRVMTIAPGLFGTPLLTSL------PEKVCNFLASQVPFPSRLGDPAEYAH--LV 237 LAP +RV +AP + TPLL + PE FL + +P RL +P + A+ L Sbjct: 177 LAPDRVRVCGLAPVMGATPLLETFMGMPDTPENRAKFLGT-IPL-GRLCEPEDMANAALY 234 Query: 238 QAIIENPFLNGEVIRLDG 255 A E F+ G ++ +DG Sbjct: 235 LASDEANFITGVILEVDG 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: 169 Number of extensions: 7 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: 256 Length adjustment: 24 Effective length of query: 237 Effective length of database: 232 Effective search space: 54984 Effective search space used: 54984 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