Align Putative pterin-4-alpha-carbinolamine dehydratase; PHS; EC 4.2.1.96; 4-alpha-hydroxy-tetrahydropterin dehydratase; Pterin carbinolamine dehydratase; PCD (uncharacterized)
to candidate WP_078427800.1 BK574_RS05195 pterin-4-alpha-carbinolamine dehydratase
Query= curated2:Q96YL0 (93 letters) >NCBI__GCF_002019605.1:WP_078427800.1 Length = 108 Score = 67.4 bits (163), Expect = 4e-17 Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 1/92 (1%) Query: 1 MKKLTEKEIREELNKMKGWSLKGNV-IEKTFLFHDFKEAVNFLNKVQPIADSMNHHPDVC 59 ++KLT +EI LN K W L IEK + FH + + + F+ K+ +++ MNHHP + Sbjct: 10 VEKLTVQEIEIFLNTYKDWKLVDEKWIEKKYRFHAYLDGIEFVQKIAQVSEEMNHHPFIS 69 Query: 60 IYYNKVIVQLTTHDAGGITDLDVELAKKIDEL 91 I Y + V+L++ G+T LD +LA++ D + Sbjct: 70 IDYKLIRVKLSSWKENGLTALDTKLAEEYDAI 101 Lambda K H 0.318 0.136 0.393 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: 28 Number of extensions: 2 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: 93 Length of database: 108 Length adjustment: 11 Effective length of query: 82 Effective length of database: 97 Effective search space: 7954 Effective search space used: 7954 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: 39 (20.8 bits) S2: 39 (19.6 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