Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_027722693.1 H589_RS0114445 inositol monophosphatase
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000425265.1:WP_027722693.1 Length = 261 Score = 99.0 bits (245), Expect = 9e-26 Identities = 72/226 (31%), Positives = 110/226 (48%), Gaps = 9/226 (3%) Query: 32 EVSSKPDMTPVSDADLATEEALREKIATARPADSILGEEFGGDVEFSGRQWIIDPIDGTK 91 ++ K + V++ DLA E+ L+E+++ P S L EE GD + R WIIDP+DGT Sbjct: 28 DIQHKGRIDLVTETDLAVEQFLKEELSKILPDSSFLAEETSGDADLVNRTWIIDPLDGTT 87 Query: 92 NYVRGVPVWATLIALLDNGKPVAGVISAPALARRWWASEGAGAWRTFNGSSPRKLSVSQV 151 N+ G+P+ AT +AL +N + V G+++ P L + A G GA+ NG + + VS Sbjct: 88 NFAHGLPMVATSVALWENDQVVLGIVNLPILNEVFTALRGEGAF--MNG---QPIHVSDC 142 Query: 152 SKLDDASLSFS---SLSGWAERDLRDQFVSLTDTTWRLRGYGDFFSYCLVAEGAVDIAAE 208 KL+++ ++ ++ E L L T R +A G D E Sbjct: 143 DKLENSLIATGFPYAIEEHTEFILSALGKVLLQTQGVRRPGAAALDLAYLACGRYDGYYE 202 Query: 209 PEVSLWDLAPLSILVTEAGGKFTSLA-GVDGPHGGDAVATNGILHD 253 + WD A +LV EAGG T G + +ATNG +HD Sbjct: 203 NSLKPWDTAAGWLLVEEAGGTVTEYGKGNYDLFSKNILATNGRMHD 248 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: 164 Number of extensions: 10 Number of successful extensions: 2 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: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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