Align histidinol phosphate phosphatase subunit (EC 3.1.3.15) (characterized)
to candidate 8500182 DvMF_0940 histidinol phosphate phosphatase HisJ family (RefSeq)
Query= metacyc::MONOMER-14284 (267 letters) >FitnessBrowser__Miya:8500182 Length = 274 Score = 140 bits (353), Expect = 3e-38 Identities = 88/269 (32%), Positives = 138/269 (51%), Gaps = 19/269 (7%) Query: 2 VDSHVHTPLCGHAEGHPEAYLEE----ARAKGLKGVVFTDHSPMPPWYD--PESRMRLEA 55 VD H HT + H +A +EE A +G++ F++HSP P Y + R +L A Sbjct: 4 VDLHTHT-----SHSHGQATVEEMFAIAMDRGMEVFGFSEHSPRPLAYSYPKDYREKLTA 58 Query: 56 -LPFYLLALERVRERAQD-LYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAW 113 P Y+ + + QD V +GLE D+ PG E F A+ + RYPFDY+IG +H+LG W Sbjct: 59 GFPRYVDEVRALAAGRQDGKTVLLGLEMDWLPGQEPFTAETIHRYPFDYIIGGIHFLGTW 118 Query: 114 PLDHP-DHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEAL-- 170 D D ++ A + F YF + + SG+F+ H D+ K F E L Sbjct: 119 GFDCTVDDWKDLAPEQANDAFERYFDSLRRMGASGMFNIAAHPDIIKIFAVDAFHEWLDR 178 Query: 171 ---LELAEPALRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHR 227 + AL + AG+ +++++AGLR+ KE+YP P ++ AREL + + GSDAH Sbjct: 179 PESRQRVRDALATLRAAGMAMEISSAGLRKLCKEIYPCPTIMEMARELELPITFGSDAHC 238 Query: 228 PEEVGFAFPEVQALLAGLGFREAYYFVEG 256 V + F +++ G+ + +F +G Sbjct: 239 TSTVAWGFDQLEEYARRFGYTHSVWFQKG 267 Lambda K H 0.322 0.141 0.436 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: 232 Number of extensions: 14 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: 267 Length of database: 274 Length adjustment: 25 Effective length of query: 242 Effective length of database: 249 Effective search space: 60258 Effective search space used: 60258 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 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