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 Ga0059261_2637 Ga0059261_2637 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Korea:Ga0059261_2637 Length = 247 Score = 107 bits (266), Expect = 3e-28 Identities = 83/252 (32%), Positives = 122/252 (48%), Gaps = 26/252 (10%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAP----ADV 65 G VAV+TGGA+G+G A AER+ +GA + D+ + EA A C FA D Sbjct: 11 GRVAVVTGGAAGIGRAAAERMAAEGAQVSVWDISD---EALA-----GCDFAAHTAKVDQ 62 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 + E V A A + GR+D+ V AGI + T +T+ + +Q+V+ +NL GT Sbjct: 63 SDEAQVIAAAADVAARLGRLDILVVSAGITGPNTTL-----ETYPSDAWQQVMAINLNGT 117 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185 F + V M N G I+N ASVA EG +AYS SK G++G+T + ++ Sbjct: 118 FFCDKAVIPHMKANG------YGRIVNIASVAGKEGNPNASAYSTSKAGVIGLTKSLGKE 171 Query: 186 LAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLV--QAIIEN 243 LA I V + P T + + + +F+ S++P R G E A ++ A E Sbjct: 172 LAKDNITVNAVTPAAVKTAIFDQMTQAHIDFMLSKIPM-GRFGTVDENAAMICFLASEEA 230 Query: 244 PFLNGEVIRLDG 255 F G V G Sbjct: 231 SFSTGAVFDTSG 242 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: 152 Number of extensions: 11 Number of successful extensions: 4 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: 247 Length adjustment: 24 Effective length of query: 237 Effective length of database: 223 Effective search space: 52851 Effective search space used: 52851 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