Align BadH (characterized)
to candidate WP_047007388.1 AAW01_RS11455 SDR family oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001010925.1:WP_047007388.1 Length = 266 Score = 159 bits (403), Expect = 4e-44 Identities = 98/266 (36%), Positives = 136/266 (51%), Gaps = 12/266 (4%) Query: 1 MARLQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLD-AAEKVAGAIRDAGGTA 57 M R KT V+TG G G+G + FA EGA V D+ LD + VA +R G Sbjct: 1 MGRFTGKTIVVTGSGKEKGLGQGILQAFADEGANCVVSDVRLDDEVDGVADELRQRGAKV 60 Query: 58 EAVRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDI-FKPFTKTEPG-EWERLIAINL 115 V+CD++D S A +A G VD+ VNNAG KP + EW++++A+NL Sbjct: 61 ATVQCDVSDAASCQALVAQALDHFGSVDVFVNNAGIGFKMKPLLDVDTADEWDQVLAVNL 120 Query: 116 TGALHMHHAVLPGMVER-RHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHA 174 +GA + A MV+ + GRI+NIAS AA+ G Y + K G+V ++ A E Sbjct: 121 SGAFYCTQAAARAMVDAGKGGRIINIASQAAKTGFPHLPAYVSSKHGMVGLTRASAVELG 180 Query: 175 RHGITVNVVCPGPTDTALLADVTS------GAANPEKLIEAFTKAIPLGRLGKPDDLAGA 228 HGITVN +CP T L A G A E + P+GR G P D A A Sbjct: 181 AHGITVNAICPNHVTTGLGAQQNEYFSKLLGFAKVEDYLANMAAKNPMGRPGLPSDTAAA 240 Query: 229 IAFFGSDDAGFITGQVLSVSGGLTMN 254 + SD+A ++TG+ L++SGG M+ Sbjct: 241 CLWLASDEAVYVTGEALNISGGEEMH 266 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: 198 Number of extensions: 13 Number of successful extensions: 5 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: 266 Length adjustment: 24 Effective length of query: 231 Effective length of database: 242 Effective search space: 55902 Effective search space used: 55902 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 24 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