Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_083509493.1 APY04_RS04980 inositol monophosphatase
Query= curated2:P56160 (259 letters) >NCBI__GCF_001541235.1:WP_083509493.1 Length = 263 Score = 110 bits (276), Expect = 2e-29 Identities = 82/260 (31%), Positives = 129/260 (49%), Gaps = 12/260 (4%) Query: 5 LQLALELAEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGL 63 + + + A KAG+ L+ D+ LQV K VT AD AEE+I + ++ P Sbjct: 7 MNVMIGAARKAGRSLSRDFGEVEQLQVSVKGPGNFVTAADLRAEEIIYRELAKARPGYSF 66 Query: 64 FGEEFDEHPSGNGR--RWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGE 121 EE E G+ R RWI+DP+DGT +F+HGVP++ + I LE EG + G+I P E Sbjct: 67 LMEERGE-VVGDDRTHRWIVDPLDGTTNFLHGVPMFAISIGLEREGQLVAGLIYNPISDE 125 Query: 122 LYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRID------A 175 ++ AE+G G F+N A + + +V T ++ H V + A Sbjct: 126 MFTAEKGKGTFLNDRRRLRVAARKRLSDALVTTGIPHI--GRQGHAVFKREAHAVFPQVA 183 Query: 176 GLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGE 235 G+ R VA+GR ++ ++ + PWD AA I +V EAGG D G ++ Sbjct: 184 GVRRTGSAALDLAWVAAGRFDLYWERGIKPWDMAAGILMVREAGGTVTDLSGASDMLVHG 243 Query: 236 GLVSANNAMGRNLIAAIGNG 255 +V++N+A+ + + I G Sbjct: 244 EVVASNSALHKEFLPLIAAG 263 Lambda K H 0.319 0.138 0.415 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: 173 Number of extensions: 10 Number of successful extensions: 3 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: 259 Length of database: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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 (21.7 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