Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_072908911.1 BUB13_RS11515 inositol monophosphatase
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_900142125.1:WP_072908911.1 Length = 265 Score = 66.6 bits (161), Expect = 5e-16 Identities = 60/198 (30%), Positives = 90/198 (45%), Gaps = 11/198 (5%) Query: 40 VTDADRAVESDVRQTLGRDRPGDGVLGEEFGGSTTFTGRQWIVDPIDGTKNFVRGVPVWA 99 V++ DR E + + LG P G GEE G S + R W++DP+DGT NF+ G+ + Sbjct: 42 VSEVDRHSEDLLLKGLGNLLPEAGFYGEETGISGSSKLR-WVIDPLDGTSNFLSGLDQFC 100 Query: 100 SLIALLEDGVPSVGVVSAPALQRRWWAARGRGAFASVDGARPHRLSVSSVAELHSASLSF 159 +AL +G +GVV PA + + A RG+G F + D P + L F Sbjct: 101 ISVALEVEGQTELGVVLRPASKECFTALRGQGLFRN-DHRCPQVTDLPLQQALIGTGFPF 159 Query: 160 SSLSGWARPGLRERFIGLTDTVWRVRAYGDF----LSYCLVAEGAVDIAAEPQVSVWDLA 215 S R E F + ++ R F L VA G + E + +D+A Sbjct: 160 RS-----RDLSAEFFACAEEVLYASRGLRRFGAAALDLSYVAAGFLQGFWESDLEPYDVA 214 Query: 216 ALDIVVREAGGRLTSLDG 233 A I +RE+G +T+ G Sbjct: 215 AALIFLRESGCIVTNRSG 232 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: 135 Number of extensions: 9 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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 10 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