Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_089323706.1 CHB58_RS08620 3'(2'),5'-bisphosphate nucleotidase
Query= curated2:P56160 (259 letters) >NCBI__GCF_900188395.1:WP_089323706.1 Length = 274 Score = 77.4 bits (189), Expect = 3e-19 Identities = 75/246 (30%), Positives = 108/246 (43%), Gaps = 28/246 (11%) Query: 5 LQLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGLF 64 L +A+ A KAG + + R V K D++P+TEADR + ++I + FP Sbjct: 5 LFVAITTALKAGDAIMKIY-ERDFTVEEKADNSPLTEADRVSHKIIVTHLH-DFPVLSEE 62 Query: 65 GEEFDEHPSGNGRR-WIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGELY 123 G+E N + WI+DP+DGT+ FI + V IA +G LGV+ PA+G LY Sbjct: 63 GKEIPYEERKNWEKLWIVDPLDGTKEFIKRNGEFTVNIAFVEKGVPVLGVVYAPAIGVLY 122 Query: 124 QAERGSGAFM--NG------------------SPVQVSAIAENSASTVVFTEKEYLLDPP 163 +G GAF NG S V VS + +V +P Sbjct: 123 YGGQGFGAFKVENGDFSFLEDITSSEVFWRELSKVAVSLPVIDDRKEIVVVASRSHRNPE 182 Query: 164 SNHPVDQLRIDAGLVR--GWGDCYGHMLVASGRAEV--AVDKIMSPWDCAAVIPIVEEAG 219 + + Q+ G V+ G VA G+A+V + M WD AA +VE AG Sbjct: 183 TEEFIRQIEKKYGKVKTISQGSSLKLTAVAEGKADVYPRIAPTME-WDTAAGQAVVEAAG 241 Query: 220 GCCFDY 225 G +Y Sbjct: 242 GKVVEY 247 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: 160 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 234 Effective length of database: 249 Effective search space: 58266 Effective search space used: 58266 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