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 N515DRAFT_3783 N515DRAFT_3783 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Dyella79:N515DRAFT_3783 Length = 255 Score = 244 bits (623), Expect = 1e-69 Identities = 129/249 (51%), Positives = 168/249 (67%), Gaps = 2/249 (0%) Query: 13 AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72 A+ITGGASGLG A A+ LV G L D+ G+ A+ LG + F DVTSE V Sbjct: 8 AIITGGASGLGYAVAQHLVAAGGQVALFDVNEDKGQEAARALGASAHFFRTDVTSEDGVS 67 Query: 73 TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLV 132 +A A+ G ++V +NCAGI A + L K L F + VNL+G+FNV + Sbjct: 68 ANVAAAREAMGGLNVVMNCAGILGAGRV--LGKEGPMPLGTFASTVMVNLVGSFNVAKAA 125 Query: 133 AGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIR 192 A M NE + G+RGVI+NTASVAA+EGQ+GQAAYSASKGG+VGMTLP+AR+L+ GIR Sbjct: 126 AALMQSNEAGEDGERGVIVNTASVAAYEGQIGQAAYSASKGGVVGMTLPMARELSRFGIR 185 Query: 193 VMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIR 252 V TIAPG+F TP++ +P +V L++ +PFPSRLG P E+A LV I+ N ++NGE IR Sbjct: 186 VATIAPGIFWTPMVDGMPPQVQESLSASIPFPSRLGRPEEFASLVAFILTNRYINGETIR 245 Query: 253 LDGAIRMQP 261 LDGA+R+QP Sbjct: 246 LDGAVRLQP 254 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: 214 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 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