Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_011779688.1 MVAN_RS12355 inositol monophosphatase
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000015305.1:WP_011779688.1 Length = 302 Score = 96.7 bits (239), Expect = 5e-25 Identities = 69/205 (33%), Positives = 102/205 (49%), Gaps = 11/205 (5%) Query: 41 PVSDADLATEEALREKIATARPADSILGEEFGGDVEFS-GR-QWIIDPIDGTKNYVRGVP 98 PV+ D TE LR+++A RP D+ILGEE GG V+ + GR W++DPIDGT N++ G+P Sbjct: 75 PVTVVDTETERLLRDRLAELRPGDAILGEEEGGSVDVADGRLTWVLDPIDGTVNFLYGIP 134 Query: 99 VWATLIALLDNGKPVAGVISAPALARRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDAS 158 +A + + +G VAG ++ A + A+ G GA G L+ + + D S Sbjct: 135 AYAVSVGVRRDGVSVAGAVADVAAGAVYSAALGHGAGVRRGG----VLTPLRCTAATDLS 190 Query: 159 LSFSSLSGWAERDLRDQ----FVSLTDTTWRLRGYGD-FFSYCLVAEGAVDIAAEPEVSL 213 ++ ER+ R + L +R G C VA G +D E +V L Sbjct: 191 MALVGTGFSYEREHRQRQGEIAARLLPDVRDVRRMGSCALDLCAVAAGRLDAYYEDDVHL 250 Query: 214 WDLAPLSILVTEAGGKFTSLAGVDG 238 WD A +++ TEAG A DG Sbjct: 251 WDWAAAALIATEAGAHVRPPATGDG 275 Lambda K H 0.315 0.133 0.396 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: 186 Number of extensions: 8 Number of successful extensions: 3 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: 260 Length of database: 302 Length adjustment: 26 Effective length of query: 234 Effective length of database: 276 Effective search space: 64584 Effective search space used: 64584 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 (21.6 bits) S2: 47 (22.7 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