Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_013429993.1 CALKRO_RS05030 histidinol-phosphatase HisJ family protein
Query= BRENDA::Q02150 (269 letters) >NCBI__GCF_000166775.1:WP_013429993.1 Length = 266 Score = 151 bits (381), Expect = 2e-41 Identities = 89/262 (33%), Positives = 142/262 (54%), Gaps = 11/262 (4%) Query: 5 DYHFHSHFSADSEELPRKHVTEAIAHGLEEICFTEHRDFYFPGMDF---SLNLPEYFQEI 61 DYH HS+FS+DS V +AI LEEI FT+H D +P + + +N +Y E Sbjct: 3 DYHIHSNFSSDSNMNMEDAVKKAIELNLEEIAFTDHMDLLYPPVSYPVWDINYEDYMNEF 62 Query: 62 NRLQAEFKDKIKIKIGLEMGIDLRFKSEINQFIDSAPFDFVIASVHEIGDIEVYDGTEFY 121 ++ ++ KIKIK+G E+G+ + + ++S FDFVIAS H + ++ DG FY Sbjct: 63 YAIKKKYSSKIKIKLGSEVGLQPHSIEKSLEILNSYSFDFVIASTHVVDFQDLADGV-FY 121 Query: 122 LQKIKEEAQREYLLACLDVVQNFENYNSFGHLDYVARYGPYTDKSIKFAENREILFEILR 181 K K++A Y L+++++F+ + +GHLD V RYG Y +K + E +++ EIL+ Sbjct: 122 QGKTKQQAYIRYFEETLNLIKSFDKFCVYGHLDIVKRYGDYENKDLDKEEYWDLIDEILK 181 Query: 182 ALASKEKALEINTRLF----DDPKTEQFYSDLLINFKKLGGKFITLGTDSHIAKRDWLSI 237 L K K +E+NT F P E ++ F +LGG+ ITLG+D+H + Sbjct: 182 LLIFKGKGIEVNTSGFRYGLGMPHPEY---KIIKRFYELGGEIITLGSDAHSTEYIAYMF 238 Query: 238 HKARTLIKKAGFHELATFSGMK 259 + ++K GF L F ++ Sbjct: 239 NYTVDMLKSIGFKYLTKFENLE 260 Lambda K H 0.322 0.139 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: 271 Number of extensions: 19 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: 269 Length of database: 266 Length adjustment: 25 Effective length of query: 244 Effective length of database: 241 Effective search space: 58804 Effective search space used: 58804 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 Jul 26 2024. The underlying query database was built on Jul 25 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