Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_011386064.1 AMB_RS18775 3'(2'),5'-bisphosphate nucleotidase
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_000009985.1:WP_011386064.1 Length = 258 Score = 100 bits (249), Expect = 3e-26 Identities = 78/222 (35%), Positives = 107/222 (48%), Gaps = 21/222 (9%) Query: 28 DLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFGGSTTF----TGRQWIVD 83 D + K D +PVT+AD E+ + L PG V+ EE + T +G W+VD Sbjct: 32 DFAVRDKTDSSPVTEADERAEAIILPGLAALTPGVPVVAEESVAAGTIPAIGSGPFWLVD 91 Query: 84 PIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAARGRGAF-ASVDGARP- 141 P+DGTK F++ + I L+ DGVP +GVV APA + W+ G AF +G RP Sbjct: 92 PVDGTKEFIKRNGEFTVNIGLIRDGVPVLGVVLAPA-RGELWSGTGATAFKEDANGRRPI 150 Query: 142 --HRLSVSSVAELHSAS-LSFSSLSGWARPGLRERFIGLTDTVWRVRAYGDFLSYCLVAE 198 L S + S S SL W +F G T + G L +CLVAE Sbjct: 151 ACRPLPASGAVIMTSRSHREPESLDKW-----MAQFPGAT-----LGFAGSSLKFCLVAE 200 Query: 199 GAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLDGVAGPHG 239 GA D+ S WD+AA V+ AGG +T+ DG+ +G Sbjct: 201 GAADLYPRFGPTSEWDIAAASAVLMAAGGSVTTFDGLPMAYG 242 Lambda K H 0.319 0.136 0.414 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: 183 Number of extensions: 13 Number of successful extensions: 4 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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