Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_027459140.1 K420_RS0117200 HAD family hydrolase
Query= reanno::BFirm:BPHYT_RS03625 (228 letters) >NCBI__GCF_000519045.1:WP_027459140.1 Length = 222 Score = 232 bits (592), Expect = 4e-66 Identities = 115/222 (51%), Positives = 150/222 (67%), Gaps = 2/222 (0%) Query: 3 NLALFDLDHTLIPTDSDHEWGRFMVKHGMVDAENFARENDRFFADYKAGKLDIHAYLIAM 62 NLALFDLD+TL+ DSD EW +F++ G+VD E +N F+ YKAG LDI+ +L Sbjct: 2 NLALFDLDNTLLAGDSDFEWAQFLISKGVVDREVQEAKNIEFYEHYKAGTLDIYEFLAFQ 61 Query: 63 LTPLSKYTRAQLADFHAQYMHEVIKPAIFPVALELVKQHRETGDLCCVVTATNEFITRPI 122 L PL++++RA+L +H +Y+ I+P + A LV +H GDLC +VTATN F+T PI Sbjct: 62 LAPLARHSRAELDAWHQEYVEHHIRPIMTVKARTLVLEHLAAGDLCAIVTATNSFVTGPI 121 Query: 123 AQAFGVDALIACEAETVDGEPHSPYTGRPTGTPSYKEGKIVRTEAWLASLGKTWSDFERS 182 A+ FG+ LI VD +TG+PTGTPS++ GKI R E WL SLG W F+ S Sbjct: 122 AREFGIGHLIG-TIPAVD-VATGAFTGQPTGTPSFQGGKITRVEHWLESLGLWWGSFDHS 179 Query: 183 YFYSDSHNDIPLLEKVTDPIATNPDDTLRAHAQAKGWRILEL 224 YFYSDSHND+PLL+KVT P+A +PDD LRAHA +GW IL L Sbjct: 180 YFYSDSHNDLPLLQKVTKPVAVDPDDKLRAHADRQGWTILSL 221 Lambda K H 0.320 0.135 0.419 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: 189 Number of extensions: 7 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: 228 Length of database: 222 Length adjustment: 22 Effective length of query: 206 Effective length of database: 200 Effective search space: 41200 Effective search space used: 41200 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: 46 (22.3 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