Align BadH (characterized)
to candidate GFF2310 Psest_2358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__psRCH2:GFF2310 Length = 252 Score = 154 bits (389), Expect = 2e-42 Identities = 96/255 (37%), Positives = 137/255 (53%), Gaps = 13/255 (5%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNL-DAAEKVAGAIRDAGGTAEAVR 61 R +TA+ITG GIG AT A EGA++ + + D A ++ I GG A A+ Sbjct: 5 RFAGQTALITGAATGIGRATALALAAEGARVWINHRDQHDLANQLVEQITANGGDAWAIE 64 Query: 62 CDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHM 121 D++D +V AA+ T G +D+LVNNAG + KPF +T +W ++ ++L G Sbjct: 65 ADVSDPAAV-AAMFETIEAQGSLDLLVNNAGVILEKPFLETSEADWAMVLGVDLGGVYRC 123 Query: 122 HHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVN 181 L M RR G IVN+ASD +G Y K G++ +++LARE A GI VN Sbjct: 124 CRHALAQMQPRRSGAIVNVASDLGFLGREQYVAYCTAKAGVIGLTRSLAREFAADGIRVN 183 Query: 182 VVCPGPTDTALLADVTSGAANPEKLIE---AFTKAIPLGRLGKPDDLAGAIAFFGSDDAG 238 V PGP TA++ +PE + + A AIP+ RLG P+++A AI F S A Sbjct: 184 GVAPGPIATAMV--------SPEHMSDEWMAKELAIPMARLGTPEEVAAAIVFLLSPQAS 235 Query: 239 FITGQVLSVSGGLTM 253 + TGQ+L +GG M Sbjct: 236 YFTGQLLGPNGGSWM 250 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: 159 Number of extensions: 8 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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