Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_043291579.1 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_000016205.1:WP_043291579.1 Length = 262 Score = 91.3 bits (225), Expect = 2e-23 Identities = 67/209 (32%), Positives = 98/209 (46%), Gaps = 13/209 (6%) Query: 31 IDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFGGSTTF---TGRQWIVDPIDG 87 + K D +PVT+AD A + + L P V+ EE S + GR W++DP+DG Sbjct: 35 VSNKADSSPVTEADLASHRVLAKHLAHLLPSCQVVSEEDPASLVYRQSAGRFWLIDPLDG 94 Query: 88 TKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAARGRGAFASVDGARPHRLSVS 147 TK F+ + IAL+++G ++GVV APA+ +W G GAF + + ++V Sbjct: 95 TKEFIARNGEFTVNIALIDEGRSTLGVVYAPAVDALYWGGSGLGAFRCICD-QTVTINVE 153 Query: 148 SVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVRAY--GDFLSYCLVAEGAVDIAA 205 AE H+ + S + L E + D + V G L +C VAEG DI Sbjct: 154 PAAEGHACRVVAS------KSHLNEATQAMIDRLGDVSLVQAGSSLKFCRVAEGEADIYP 207 Query: 206 E-PQVSVWDLAALDIVVREAGGRLTSLDG 233 WD AA V+ AGG + L G Sbjct: 208 RLAPTCEWDTAAAQAVLEGAGGAVVDLHG 236 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: 129 Number of extensions: 7 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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