Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_012969362.1 ALVIN_RS00590 HAD-IB family hydrolase
Query= reanno::Marino:GFF473 (218 letters) >NCBI__GCF_000025485.1:WP_012969362.1 Length = 218 Score = 242 bits (617), Expect = 4e-69 Identities = 118/217 (54%), Positives = 151/217 (69%) Query: 1 MTLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGF 60 M LAIFDLDNTLL GDSD+ WG +L G+VD+ EY N+RFY+EY +G LDI +L F Sbjct: 1 MPLAIFDLDNTLLDGDSDYLWGCYLARHGLVDSAEYARENERFYREYQDGTLDIQEFLRF 60 Query: 61 ALQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEP 120 +L+PL H E L A R F+E+++ P+M A L++ H+ G TL+IITATN FVT P Sbjct: 61 SLRPLREHPRERLEALRARFLEEQIEPIMTPAARALVERHQSAGDTLLIITATNAFVTAP 120 Query: 121 IAEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDS 180 IAE G+ HLIAT P +G YTGEV G PSF++GKV RL+ WL+ L G+ FYSDS Sbjct: 121 IAERFGVPHLIATLPAERDGVYTGEVEGVPSFREGKVERLEHWLAEQGLDLAGSCFYSDS 180 Query: 181 HNDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217 HNDLPLL++V+ P+AV+PD L A GW ++SLR Sbjct: 181 HNDLPLLERVERPIAVNPDAQLRATAETRGWPILSLR 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: 204 Number of extensions: 7 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: 218 Length adjustment: 22 Effective length of query: 196 Effective length of database: 196 Effective search space: 38416 Effective search space used: 38416 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 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