Align Pterin-4-alpha-carbinolamine dehydratase; PHS; 4-alpha-hydroxy-tetrahydropterin dehydratase; Dimerization cofactor of hepatocyte nuclear factor 1-alpha; DCoH; Dimerization cofactor of HNF1; cDcoH; Phenylalanine hydroxylase-stimulating protein; Pterin carbinolamine dehydratase; PCD; EC 4.2.1.96 (characterized)
to candidate BPHYT_RS19525 BPHYT_RS19525 pterin-4-alpha-carbinolamine dehydratase
Query= SwissProt::O73930 (104 letters) >FitnessBrowser__BFirm:BPHYT_RS19525 Length = 96 Score = 121 bits (304), Expect = 2e-33 Identities = 57/95 (60%), Positives = 72/95 (75%), Gaps = 2/95 (2%) Query: 7 RLNAEEREQLLPNLRAVGWNEVEGRDAIFKEFHFKDFNRAFGFMTRVALQAEKLDHHPEW 66 +L +E+R L L GW V RDAI ++F F DFN AFGFMTRVA++A+++DHHPEW Sbjct: 4 KLTSEQRATQLAGLH--GWQAVADRDAIQRQFKFADFNEAFGFMTRVAIKAQEMDHHPEW 61 Query: 67 FNVYNKVHITLSTHECTGLSERDINLASFIEQVAA 101 FNVYNKV ITLSTH+ GL+ERDI LA+FI+ + A Sbjct: 62 FNVYNKVEITLSTHDAGGLTERDIKLATFIDSITA 96 Lambda K H 0.321 0.134 0.405 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: 55 Number of extensions: 2 Number of successful extensions: 1 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: 104 Length of database: 96 Length adjustment: 11 Effective length of query: 93 Effective length of database: 85 Effective search space: 7905 Effective search space used: 7905 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: 39 (21.0 bits) S2: 39 (19.6 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