Align Histidinol-phosphatase; Hol-Pase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate WP_019556519.1 F612_RS0104285 HAD-IB family hydrolase
Query= SwissProt::Q9I6F6 (217 letters) >NCBI__GCF_000381085.1:WP_019556519.1 Length = 217 Score = 227 bits (579), Expect = 1e-64 Identities = 113/217 (52%), Positives = 142/217 (65%) Query: 1 MRLALFDLDNTLLAGDSDHSWGEWLCQRGLVDAAEYQARNDAFYADYVAGKLDVLAYQAF 60 M L +FDLDNTL+ GDSD+ WG +L + VDA E+ A+N+ FY DY AG LD++AYQ F Sbjct: 1 MALVIFDLDNTLIGGDSDYLWGAFLVENQYVDATEFAAQNEQFYEDYKAGTLDIMAYQRF 60 Query: 61 TQAILGRTEMAQLETWHRQFMQEVIEPIVLAKGEALLAEHRAAGDRLVIITATNRFVTGP 120 L + M L WH QFMQ IEPIVL K AL+ +H+ GDR++IITATN F+T Sbjct: 61 ALKPLSQHSMETLNEWHAQFMQTFIEPIVLPKALALVNDHKNKGDRVIIITATNTFITRR 120 Query: 121 IAERLGVETLIATECEMRDGRYTGQTFDVPCFQGGKVVRLQRWLDENGLDLEGASFYSDS 180 I R G+ L+ T E+ + RYTG+ +P FQ GKV RL WL+ + L G+ FYSDS Sbjct: 121 IGLRYGITELLGTNGEIVNKRYTGEVEGIPTFQAGKVTRLNEWLERENVSLAGSVFYSDS 180 Query: 181 LNDLPLLEKVSRPVAVDPDPRLRAEAEKRGWPIISLR 217 NDLPLL+ V PV VD D +L A+ RGWP ISLR Sbjct: 181 FNDLPLLDIVDNPVVVDGDDKLLNIAKTRGWPSISLR 217 Lambda K H 0.321 0.138 0.418 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: 176 Number of extensions: 2 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: 217 Length of database: 217 Length adjustment: 22 Effective length of query: 195 Effective length of database: 195 Effective search space: 38025 Effective search space used: 38025 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 (21.9 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