Align histidinol phosphate phosphatase subunit (EC 3.1.3.15) (characterized)
to candidate WP_012283095.1 HM1_RS09170 histidinol phosphate phosphatase HisJ family
Query= metacyc::MONOMER-14284 (267 letters) >NCBI__GCF_000019165.1:WP_012283095.1 Length = 253 Score = 153 bits (387), Expect = 3e-42 Identities = 94/256 (36%), Positives = 134/256 (52%), Gaps = 17/256 (6%) Query: 1 MVDSHVHTPLCG---HAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYDPESRMRLEALP 57 +VD HVH G H AYLE AR +G+ V F DH YD + Sbjct: 2 LVDYHVHAMGHGTSRHTVEEISAYLETARMRGIAQVGFADHDRYLDEYDVD--------- 52 Query: 58 FYLLALERVRERAQDLYVGIGLEADFHPGTEGFLAQLLRRYPFDYVIGSVHYLGAWPLDH 117 A+ R D+ V +G+E D+ + L + RYPFDYVIGSVH + W D Sbjct: 53 ----AICEAALRYPDVQVRLGVEIDYIRNADVELRAMTSRYPFDYVIGSVHKIEDWDFDC 108 Query: 118 PDHQEEYAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLPEEALLELAEPA 177 + + Y ++ +++R YF V + A GLF IGHLDL K F R + +++ELA A Sbjct: 109 VEFIDRYDRWEMDDLYRTYFDHVREVAEKGLFSFIGHLDLIKIFNFR-SKGSIVELAAEA 167 Query: 178 LRAVAEAGLFLDVNTAGLRRPAKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPE 237 ++A+ +AGL ++NT GL +P E+YP LL R E+GI ++L SDAH EVG + Sbjct: 168 IQAIRKAGLPCEINTNGLNKPVAEMYPQRVLLERCFEVGIPIILSSDAHFAHEVGRDLDK 227 Query: 238 VQALLAGLGFREAYYF 253 + L +G+R+ F Sbjct: 228 ARDLAWSVGYRQVATF 243 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: 222 Number of extensions: 14 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: 267 Length of database: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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