Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_012506300.1 PAES_RS08740 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= BRENDA::P95189 (260 letters) >NCBI__GCF_000020625.1:WP_012506300.1 Length = 263 Score = 60.8 bits (146), Expect = 3e-14 Identities = 68/225 (30%), Positives = 97/225 (43%), Gaps = 42/225 (18%) Query: 28 DLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEFGGSTTFTGRQ-----WIV 82 D ++ K D +P+T AD+A + Q L VL EE G + + R W+V Sbjct: 33 DHGVELKGDDSPLTLADKAAHRVIMQML--QDTALPVLSEE-GRNIPYVERAQWERFWMV 89 Query: 83 DPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWWAARGRGAF--------- 133 DP+DGTK F+ + IAL+E G P +GVV P L + GRGA Sbjct: 90 DPLDGTKEFISRNGEFTVNIALVEHGKPVMGVVYVPVLDELYVGKAGRGALLIRNAAAEP 149 Query: 134 ---------ASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRV 184 A+ DG +R+ V S + L+ +L+F P + + V R Sbjct: 150 WETVTLPCGAAGDGV--YRV-VGSRSHLNDETLAFVEELRAEHPEI--------EMVQR- 197 Query: 185 RAYGDFLSYCLVAEGAVDIAAEPQVSV-WDLAALDIVVREAGGRL 228 G L C+VA G D +++ WD AA VV AG R+ Sbjct: 198 ---GSSLKICMVAAGDADCYPRFGLTMEWDTAAGHAVVNAAGKRM 239 Lambda K H 0.319 0.136 0.414 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: 124 Number of extensions: 3 Number of successful extensions: 2 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: 260 Length of database: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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