Align Histidinol-phosphatase (EC:3.1.3.15) (characterized)
to candidate WP_020562319.1 A3OW_RS0104935 HAD-IB family hydrolase
Query= reanno::Marino:GFF473 (218 letters) >NCBI__GCF_000372865.1:WP_020562319.1 Length = 228 Score = 260 bits (664), Expect = 2e-74 Identities = 119/217 (54%), Positives = 157/217 (72%) Query: 1 MTLAIFDLDNTLLAGDSDHAWGEFLVEEGIVDAEEYRLANDRFYQEYLNGELDILHYLGF 60 M+LAIFDLDNTL+A DSD+ WG+FLV++GIVD +Y AN RFY++Y G LDI+ +L F Sbjct: 1 MSLAIFDLDNTLIADDSDYLWGQFLVDQGIVDKHQYEAANARFYEDYKQGRLDIVEFLRF 60 Query: 61 ALQPLASHNMEELLAWREAFMEKKVRPMMQATANTLLDSHREQGHTLMIITATNRFVTEP 120 +L+PL H +L AWR+ F+ + + P++ A L+ H+ +G TL++ITATNRFVTEP Sbjct: 61 SLRPLTLHAPRQLFAWRDRFVSEIITPILLEPARELIAKHKSRGDTLLVITATNRFVTEP 120 Query: 121 IAEALGIEHLIATEPELVNGRYTGEVAGTPSFQDGKVTRLDDWLSAHNRTLEGAWFYSDS 180 I + GI+HL+AT PE V+GRYTG G P FQ+GKV L WL + T+ +WFYSDS Sbjct: 121 IVKLYGIDHLLATPPEFVDGRYTGNFVGEPCFQEGKVRLLQQWLEDNRETMNDSWFYSDS 180 Query: 181 HNDLPLLKKVDNPVAVDPDPTLAQYARDNGWKVMSLR 217 HNDLPLL +VD+ VAVDPD L +AR GW ++SLR Sbjct: 181 HNDLPLLNRVDHAVAVDPDEKLKAHARKAGWPIISLR 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: 226 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: 218 Length of database: 228 Length adjustment: 22 Effective length of query: 196 Effective length of database: 206 Effective search space: 40376 Effective search space used: 40376 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: 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