Align Pterin-4-alpha-carbinolamine dehydratase 2; PHS 2; 4-alpha-hydroxy-tetrahydropterin dehydratase 2; DcoH-like protein DCoHm; Dimerization cofactor of hepatocyte nuclear factor 1 from muscle; HNF-1-alpha dimerization cofactor; EC 4.2.1.96 (characterized)
to candidate WP_011383005.1 AMB_RS02910 4a-hydroxytetrahydrobiopterin dehydratase
Query= SwissProt::Q9CZL5 (136 letters) >NCBI__GCF_000009985.1:WP_011383005.1 Length = 132 Score = 111 bits (277), Expect = 4e-30 Identities = 53/116 (45%), Positives = 79/116 (68%), Gaps = 5/116 (4%) Query: 22 AALRSPGASRAAMSSDAQW---LTAEERDQLIPGLKAAGWSELSERDAIYKEFSFKNFNQ 78 A R P + + D + L+ ER + GL AGW+E+ RDAI + F +F++ Sbjct: 14 AGTRGPHSFDSTRQGDGKMIARLSGSERTSALAGL--AGWTEVEGRDAISRSLRFADFSE 71 Query: 79 AFGFMSRVALQAEKMNHHPEWFNVYNKVQITLTSHDCGGLTKRDVKLAQFIEKAAA 134 AF FM+R+A+ AE+MNHHPEWFNV+N+V ITL++HD GG+T++D+ LA+ I+ AA+ Sbjct: 72 AFAFMTRIAMAAERMNHHPEWFNVWNRVDITLSTHDVGGVTQKDISLARAIDAAAS 127 Lambda K H 0.318 0.127 0.375 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: 52 Number of extensions: 1 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: 136 Length of database: 132 Length adjustment: 15 Effective length of query: 121 Effective length of database: 117 Effective search space: 14157 Effective search space used: 14157 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: 41 (21.8 bits) S2: 42 (20.8 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