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 HSERO_RS20035 HSERO_RS20035 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS20035 Length = 254 Score = 244 bits (623), Expect = 1e-69 Identities = 137/254 (53%), Positives = 167/254 (65%), Gaps = 3/254 (1%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTS 67 ++G A++TGGASGLG T +LV GA +LD+ +A A +L C D+T Sbjct: 3 LQGQAALVTGGASGLGAETVRQLVQAGARVSILDVNMEAAQALADEL--RCHAVRCDITD 60 Query: 68 EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127 V+TAL A+ G + +NCAGI A + K G+ LEDF R+++VNL+GTFN Sbjct: 61 SDSVETALQAAQQTNGAPRILINCAGIGGAKRMVG-KDGKPMPLEDFSRIVNVNLIGTFN 119 Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 VIRL A M E G+RGVI+ TASVAAF+GQVGQA Y+ASKGGI MTLP+ARDLA Sbjct: 120 VIRLAAARMAAAEALAEGERGVIVATASVAAFDGQVGQAGYAASKGGITAMTLPLARDLA 179 Query: 188 PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLN 247 GIRV+TIAPGLF TPLL LPE+V LAS +PFP RLG EYA L I N LN Sbjct: 180 QYGIRVVTIAPGLFLTPLLYKLPEEVQQSLASSIPFPKRLGKAEEYAQLALHIATNLSLN 239 Query: 248 GEVIRLDGAIRMQP 261 GEVIRLDGA+R+ P Sbjct: 240 GEVIRLDGALRLAP 253 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: 231 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: 254 Length adjustment: 24 Effective length of query: 237 Effective length of database: 230 Effective search space: 54510 Effective search space used: 54510 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