Align Probable histidinol-phosphatase; HolPase; EC 3.1.3.15 (uncharacterized)
to candidate WP_012282069.1 HM1_RS04270 histidinol phosphate phosphatase
Query= curated2:P58291 (255 letters) >NCBI__GCF_000019165.1:WP_012282069.1 Length = 257 Score = 266 bits (679), Expect = 4e-76 Identities = 120/250 (48%), Positives = 180/250 (72%) Query: 1 MVFDTHLHTLFSTDSKMNIEEAIDAGEKKNLGIIITEHIDLNYPVKGEFVFDIDKYFKEY 60 M+FDTH+HT FSTDS M I++AI+ +K++G+IIT+H+DL YP F FD+D +F+ Y Sbjct: 1 MIFDTHVHTRFSTDSIMAIDQAIEQARQKDIGLIITDHMDLAYPQPDSFTFDVDAFFRTY 60 Query: 61 NKYRSNKVLLGVEIGMGEEIKEQNKSINDKYEFDYVLGSIHLLNGLDLYEKTIYKSSPKK 120 YRS+++ LGVE+GM E+ N+ + Y FDY++GSIH+++G+++ + + K+ Sbjct: 61 EPYRSDRLRLGVEMGMRSELISHNRKLAAAYPFDYIIGSIHVVDGVEVVGERYFGRRSKR 120 Query: 121 EVFEMYFKTMLACLRCHEYIDSLAHIDYISRYAAYHDGEIYYNEYSDYIDEVLKFIVDRE 180 E ++ YF TML C++ +++IDSL HIDYI+RYA D EI Y+E+ + ID +L + +R+ Sbjct: 121 ESYDRYFDTMLECVKAYDFIDSLGHIDYIARYALVEDPEIDYDEFREQIDPILAVLAERQ 180 Query: 181 IVIEINTRRLNKKEVCENLMPIYKRYSELGGRFVTIGSDSHYKDSIGLNFKNALKMAENC 240 IEIN RRL++ V E L PIY+R++ELGGRFVT+GSD+H IG N K AL +AE C Sbjct: 181 QAIEINARRLDRPAVVEALFPIYRRFAELGGRFVTVGSDAHNPRDIGRNLKAALALAERC 240 Query: 241 NLKPVFFEKR 250 L+PV++++R Sbjct: 241 RLQPVWYKER 250 Lambda K H 0.320 0.140 0.404 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: 256 Number of extensions: 12 Number of successful extensions: 1 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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 09 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