Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate WP_011373480.1 SUDEN_RS09690 PHP domain-containing protein
Query= curated2:Q9RX45 (260 letters) >NCBI__GCF_000012965.1:WP_011373480.1 Length = 259 Score = 175 bits (443), Expect = 1e-48 Identities = 91/259 (35%), Positives = 150/259 (57%), Gaps = 8/259 (3%) Query: 4 LCDSHLHTPLCGHATGTPREYAQAALDAGLSGLCFTDHMPMPRWYDAPWRMKLEQLPEYI 63 + D H HT LC HA G EY + A++ + F +H PM +D +R+ EQ+ Y Sbjct: 2 IADLHNHTKLCNHAEGEINEYIEKAIECNIKYFGFAEHAPMN--FDPKYRISFEQMQSYE 59 Query: 64 AEIQAVQQEFAGRLDVRLGLEADFHPGTEKFVEKVLGMFDWDYVIGSVHYLGAWGFDNPE 123 I V++ + ++++ LG E D+ G E+VL DY+IGSVH++ WGFDNPE Sbjct: 60 QSILEVKELYKEKIEILLGYEVDYLRGYMD--ERVLNA-KVDYLIGSVHFINEWGFDNPE 116 Query: 124 FVAEYEERDLGGLYRDYYALVEGAARSGLFDAIGHLDLPKKFGHLDPDPV--YALHALDV 181 F+ +YE +D+ +++ Y+ +E A+S LFD +GHLDL K F + + A +AL Sbjct: 117 FIKDYENQDIDEIWQKYFDAIEEMAKSKLFDIVGHLDLIKIFKFMPKGNIAYIAKNALKA 176 Query: 182 VAGQGLALDFNTAGWRKPVAEAYPAPDLVRAAAERGIPFVLGSDAHQPGEVGFRFADAVK 241 + ++++ N AG RKP+A+ YP+ DL++ + I SDAH+P +VG + +K Sbjct: 177 IKDADMSVEINVAGLRKPIAQTYPSYDLLKEVKKLNISITFASDAHKPEQVGLFSDETMK 236 Query: 242 EIRDVG-GRTVTFRHRKMQ 259 ++++G + V +R+RK + Sbjct: 237 MVKELGFSQCVIYRNRKKE 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: 199 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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