Align BadH (characterized)
to candidate CCNA_01885 CCNA_01885 short chain dehydrogenase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Caulo:CCNA_01885 Length = 258 Score = 159 bits (401), Expect = 7e-44 Identities = 88/249 (35%), Positives = 129/249 (51%), Gaps = 5/249 (2%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62 RL+ + A +TG G+G AT A EGA +A+ DL A+ A I AGG A + C Sbjct: 10 RLEGRVAAVTGASRGLGRATAALLAAEGAMVALLDLKAHWAQAAADEIIAAGGKAVGLGC 69 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 D++DR ++ A + G D+LVNNA W++++P P +R++++ +G + Sbjct: 70 DVSDREALTATLGAVNDAHGRFDVLVNNAMWNVYEPLAAIRPESLDRMVSVGFSGVIWGM 129 Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182 A P M G IVNIAS +A++G Y K G+ ++ A E I VN Sbjct: 130 QAAAPLMAASGGGSIVNIASVSAQLGIPNGIAYCGVKAGVAGMTRAAAAELGAMNIRVNA 189 Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242 V P DT + V S E+ I PLGRLG +D+A A+ + DD+ F+TG Sbjct: 190 VAPSTVDTEGVRRVVS-----EERIAMRIGQTPLGRLGTTEDIAKAVRYLACDDSDFVTG 244 Query: 243 QVLSVSGGL 251 Q+L+V GGL Sbjct: 245 QMLTVDGGL 253 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: 172 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: 255 Length of database: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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