Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate H281DRAFT_02047 H281DRAFT_02047 HAD-superfamily subfamily IB hydrolase, TIGR01490
Query= reanno::BFirm:BPHYT_RS03625 (228 letters) >FitnessBrowser__Burk376:H281DRAFT_02047 Length = 227 Score = 250 bits (638), Expect = 2e-71 Identities = 120/223 (53%), Positives = 156/223 (69%) Query: 3 NLALFDLDHTLIPTDSDHEWGRFMVKHGMVDAENFARENDRFFADYKAGKLDIHAYLIAM 62 NLALFDLDHTL+P DSD W F+ G+ A A++ D ++ Y AG LD+ AYL Sbjct: 4 NLALFDLDHTLLPLDSDQAWAHFIAGLGIEGAARHAQDIDEYYRQYVAGTLDMAAYLDYT 63 Query: 63 LTPLSKYTRAQLADFHAQYMHEVIKPAIFPVALELVKQHRETGDLCCVVTATNEFITRPI 122 L PL++++R QL +HAQ+M EVI PAI P A ELV++H E GDLCC+VTATN F+T PI Sbjct: 64 LAPLARHSREQLDTWHAQFMQEVITPAILPAARELVQRHIEAGDLCCIVTATNVFVTAPI 123 Query: 123 AQAFGVDALIACEAETVDGEPHSPYTGRPTGTPSYKEGKIVRTEAWLASLGKTWSDFERS 182 +A G + L+ E T +P + +TG G P+++EGKI RTE+WLASLG DF +S Sbjct: 124 GKALGFEHLLGIELGTEGDDPLARFTGASVGVPTFREGKIARTESWLASLGHRLHDFPQS 183 Query: 183 YFYSDSHNDIPLLEKVTDPIATNPDDTLRAHAQAKGWRILELF 225 +FYSDS ND+PLLE+VT P+ATNPD LRA A +GW ++ELF Sbjct: 184 WFYSDSINDVPLLERVTHPVATNPDPRLRAIANERGWPVIELF 226 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: 206 Number of extensions: 10 Number of successful extensions: 1 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: 227 Length adjustment: 22 Effective length of query: 206 Effective length of database: 205 Effective search space: 42230 Effective search space used: 42230 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