Align BadH (characterized)
to candidate Pf6N2E2_1839 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase (EC 1.1.1.-)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1839 Length = 244 Score = 216 bits (549), Expect = 5e-61 Identities = 120/251 (47%), Positives = 158/251 (62%), Gaps = 11/251 (4%) Query: 1 MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60 M L + A +TGG GIG A RR A EGAK+ + ++ +AE++A + GG A V Sbjct: 3 MRALTGQRAFVTGGSKGIGEAIVRRLAAEGAKVVIAAQDMISAERLADEV---GGLA--V 57 Query: 61 RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120 R D+ D V+ + T LGP +ILVNNAG+D FTKT +W L+A+NL G Sbjct: 58 RLDVTDLLEVERVV----TMLGPFEILVNNAGYDQHDFFTKTTVEQWRYLLAVNLEGVFA 113 Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180 HA LP M +GRI+N+ S+A R GS G AVYAA KGG++AFSK++ARE+AR+GITV Sbjct: 114 STHAALPAMQAAGYGRIINVGSEAGRQGSKGGAVYAAAKGGVIAFSKSIARENARYGITV 173 Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240 NVV PGP DT LL EKL+ A + +GRLG+P+++A A+ F S DA FI Sbjct: 174 NVVAPGPVDTPLLRKALDRGG--EKLLAAMEASTLVGRLGEPNEVAAAVVFLASRDASFI 231 Query: 241 TGQVLSVSGGL 251 TG+ L VSGG+ Sbjct: 232 TGETLGVSGGM 242 Lambda K H 0.318 0.135 0.398 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: 203 Number of extensions: 11 Number of successful extensions: 3 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: 255 Length of database: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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: 46 (22.3 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