Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Dsui_2312 Dsui_2312 3-hydroxybutyrate dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__PS:Dsui_2312 Length = 260 Score = 118 bits (295), Expect = 1e-31 Identities = 78/254 (30%), Positives = 124/254 (48%), Gaps = 8/254 (3%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQ--AEKVETVAAHWRERGADVHALK 76 L K+ L+TG+ GIG A+ A A A ++++ + AE AA E G V Sbjct: 2 LSGKIALVTGSTSGIGLAVARALARNGAAVMLNGSRPAAEAEGLRAAMAAEFGVKVAYTS 61 Query: 77 ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 AD+++ + A+A A ++ G +D+LVN AG+ E EE W + AI+L ++ Sbjct: 62 ADLADAASVRALAAAAEKQLGVVDILVNNAGIQHVAAVDEFPEEKWDQLIAINLSSVFHA 121 Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 KAVLP M + G I+NIAS H P PY +KH ++G ++A+ +E A G+ N Sbjct: 122 TKAVLPGMKARNWGRIVNIASAHGLVASPFKAPYTASKHAVVGFSKAVALEVAETGITCN 181 Query: 197 AIAPGYIETQLNVDY------WNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASD 250 A+ PGY+ T L + + R L P +R + ++A +FL S Sbjct: 182 AVCPGYVRTPLVEKQVAAQAKVHNLPEDQVIRDVILAAQPNKRFLEADDLAEFVLFLCSP 241 Query: 251 EAPFINASCITIDG 264 + + + +DG Sbjct: 242 AGAGMTGAALPMDG 255 Lambda K H 0.321 0.137 0.419 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: 162 Number of extensions: 10 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: 272 Length of database: 260 Length adjustment: 25 Effective length of query: 247 Effective length of database: 235 Effective search space: 58045 Effective search space used: 58045 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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