Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_013518281.1 ALIDE2_RS17430 HAD-IB family hydrolase
Query= reanno::BFirm:BPHYT_RS03625 (228 letters) >NCBI__GCF_000204645.1:WP_013518281.1 Length = 224 Score = 218 bits (556), Expect = 6e-62 Identities = 115/223 (51%), Positives = 143/223 (64%), Gaps = 6/223 (2%) Query: 4 LALFDLDHTLIPTDSDHEWGRFMVKHGMVDAENFARENDRFFADYKAGKLDIHAYLIAML 63 LALFDLDHTL+P DSD+EWG F ++ G D E F R N F+ DY AG+LD+H Y+ Sbjct: 3 LALFDLDHTLLPLDSDYEWGEFTIRIGWTDREEFGRRNKAFYDDYVAGRLDVHDYVRFAT 62 Query: 64 TPLSKYTRAQLADFHAQYMHEVIKPAIFPVALELVKQHRETGDLCCVVTATNEFITRPIA 123 + + A HAQ+M +VI PAI A L+++HR+ GD ++TATNEFITRPIA Sbjct: 63 EAVRQRGAQAAARAHAQFMRDVIAPAIHDEARALLQRHRDAGDEIVIITATNEFITRPIA 122 Query: 124 QAFGVDALIACEAET-VDGEPHSPYTGRPTGTPSYKEGKIVRTEAWLASLGKTWSDFERS 182 QA GV L+A E E DG TG G P+ +EGK+ R E WLA G W D + S Sbjct: 123 QALGVQQLLALELERGADGW----ITGGIRGVPTMREGKVRRMEQWLAERGLRWQDVD-S 177 Query: 183 YFYSDSHNDIPLLEKVTDPIATNPDDTLRAHAQAKGWRILELF 225 FYSDS ND+PLLEKV P+ATNPD LR A+ +GW IL+LF Sbjct: 178 TFYSDSMNDVPLLEKVDHPVATNPDPRLRVLARERGWPILDLF 220 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: 187 Number of extensions: 8 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: 228 Length of database: 224 Length adjustment: 22 Effective length of query: 206 Effective length of database: 202 Effective search space: 41612 Effective search space used: 41612 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 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