Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate WP_084274610.1 B8779_RS00360 PHP domain-containing protein
Query= curated2:Q9RX45 (260 letters) >NCBI__GCF_900176045.1:WP_084274610.1 Length = 272 Score = 188 bits (477), Expect = 1e-52 Identities = 98/257 (38%), Positives = 147/257 (57%), Gaps = 20/257 (7%) Query: 6 DSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPMPRWYDAPWRMKLEQLPEYIAE 65 D H HT C HATG EY Q A+ G+ F+DH PM +D +RM LE++ Y + Sbjct: 4 DLHNHTKRCNHATGEMEEYVQRAIAEGIEIYGFSDHAPMN--FDQKYRMSLEEVDAYEKD 61 Query: 66 IQAVQQEFAGRLDVRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYL----------- 114 +Q +++++ ++++ LG E DF PG +E + D DY+IGSVH+L Sbjct: 62 VQELKEKYKNKIEILLGYEVDFLPG---LMEDRIVQADVDYLIGSVHFLPKSRKHDEILI 118 Query: 115 --GAWGFDNPEFVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFGHLDPDP 172 WGFDNPEF+ EY+ +D+ ++ DY++ +E A+SGLF +GHLDL K F Sbjct: 119 HQDLWGFDNPEFIGEYKNKDIDTIWEDYFSAIEALAKSGLFQIVGHLDLIKVFNFKPKKD 178 Query: 173 V--YALHALDVVAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGSDAHQPG 230 V A +AL + L L+ ++AG RKPV E YP+ +L+ A E IP SDAH P Sbjct: 179 VRLIAKNALKTIKENNLVLEISSAGLRKPVGEPYPSKELLEEAYELDIPITFASDAHAPE 238 Query: 231 EVGFRFADAVKEIRDVG 247 +VG++ + ++ ++VG Sbjct: 239 QVGYKLDEVMQLAKEVG 255 Lambda K H 0.322 0.142 0.455 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: 210 Number of extensions: 12 Number of successful extensions: 5 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: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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 (21.9 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