Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_009064810.1 CKL_RS01320 PHP domain-containing protein
Query= BRENDA::Q02150 (269 letters) >NCBI__GCF_000016505.1:WP_009064810.1 Length = 277 Score = 144 bits (364), Expect = 2e-39 Identities = 90/270 (33%), Positives = 144/270 (53%), Gaps = 18/270 (6%) Query: 5 DYHFHSHFSADSEELPRKHVTEAIAHGLEEICFTEHRDF-------------YFPGMDFS 51 DYH H+ FS DS + V +AI +EEICFT+H D+ Y GM + Sbjct: 4 DYHVHTEFSDDSVYEMEEVVKDAIQIKMEEICFTDHVDYGVKLDWNDKKEIQYRDGMPMA 63 Query: 52 -LNLPEYFQEINRLQAEFKDKIKIKIGLEMGIDLRFKSEINQFIDSAPFDFVIASVHEIG 110 + PEYF+ I LQ + D I IK G+E G+ + S+ + PFDF+I SVH+I Sbjct: 64 NVYYPEYFETIKELQYLYGDLIAIKKGMEFGVQVHTISQYEKLFVKYPFDFIILSVHQID 123 Query: 111 DIEVYDGTEFYLQKIKEEAQREYLLACLDVVQNFENYNSFGHLDYVARYGPYTDKSIKFA 170 ++E++ +F K ++E +Y L++V+ ++NY+ GHLD + RY + + F Sbjct: 124 NLELWT-QDFQKGKSQKEYNEKYYQELLEIVKQYKNYSVLGHLDIIIRYD--KNGTYPFE 180 Query: 171 ENREILFEILRALASKEKALEINTRLFDDPKTEQFYS-DLLINFKKLGGKFITLGTDSHI 229 + +I+ EIL+ + K +E+NT + T+ S D+L +KKLGG+ IT+G+DSH Sbjct: 181 KISDIVNEILKIVIRDGKGIEVNTSSYRYGLTDMTPSKDILTLYKKLGGEIITIGSDSHK 240 Query: 230 AKRDWLSIHKARTLIKKAGFHELATFSGMK 259 + I + ++ GF T+ M+ Sbjct: 241 KGQLGAHIENTKKVLFDMGFRYHCTYENMR 270 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: 265 Number of extensions: 12 Number of successful extensions: 5 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: 277 Length adjustment: 25 Effective length of query: 244 Effective length of database: 252 Effective search space: 61488 Effective search space used: 61488 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