Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_018232211.1 THITHI_RS0106230 HAD family hydrolase
Query= reanno::Marino:GFF473 (218 letters) >NCBI__GCF_000378965.1:WP_018232211.1 Length = 219 Score = 268 bits (684), Expect = 8e-77 Identities = 124/217 (57%), Positives = 158/217 (72%) Query: 1 MTLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGF 60 MTLAIFDLDNTL+AGDSD+ WG FL + G+VDA+ Y+ N FY++Y G LDI + F Sbjct: 1 MTLAIFDLDNTLIAGDSDYEWGRFLTDIGVVDADTYQATNRVFYEQYKAGTLDIHEFCRF 60 Query: 61 ALQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEP 120 A +PLA H++E L WR F+ +++ P++ A LL HR+ G TL+IITATN F+TEP Sbjct: 61 AFRPLAEHDVETLHGWRNRFLTERIEPLILPAAEALLARHRQAGDTLLIITATNLFITEP 120 Query: 121 IAEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDS 180 IAE LG+ L+ATEP +GRYTGE+ G P FQ GKVTRL+ WL H L+G+WFYSDS Sbjct: 121 IAERLGVNDLLATEPAFRDGRYTGELQGVPCFQGGKVTRLEAWLREHGENLDGSWFYSDS 180 Query: 181 HNDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217 HND+PLL++VDNPVAVDPD LA +A W ++SLR Sbjct: 181 HNDIPLLERVDNPVAVDPDEALADHAAARDWPIISLR 217 Lambda K H 0.318 0.135 0.408 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: 231 Number of extensions: 11 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: 218 Length of database: 219 Length adjustment: 22 Effective length of query: 196 Effective length of database: 197 Effective search space: 38612 Effective search space used: 38612 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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