Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_018125213.1 B149_RS0111010 inositol monophosphatase family protein
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000375485.1:WP_018125213.1 Length = 259 Score = 108 bits (271), Expect = 9e-29 Identities = 81/264 (30%), Positives = 129/264 (48%), Gaps = 12/264 (4%) Query: 1 MSKYADDLALALELAELA-DSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIAT 59 MS YA+ LA A + E + D + + + ++ + D+ V+D D+A EE L+E++ Sbjct: 1 MSNYAEWLAAARSIVERSGDIVRGNNLKPRNIRHKGRIDL--VTDTDVAVEEFLKEELLK 58 Query: 60 ARPADSILGEEFGGDVEFSGRQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISA 119 A P L EE GD W+IDP+DGT N+ G+P AT +AL G+ V GV++ Sbjct: 59 AFPTSRFLAEESAGDAGLQDMTWVIDPVDGTXNFAHGLPFVATSVALWHQGQVVLGVVNL 118 Query: 120 PALARRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDA--SLSFSSLSGWAERDLRDQFV 177 P + + AS G G T NG + ++VS ++++ + F G + ++ Sbjct: 119 PLMNELFAASLGGGT--TLNG---KPVTVSSTEMIEESLFATGFPYAIGEHLEGILERLR 173 Query: 178 SLTDTTWRLRGYG-DFFSYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGGKFTSLAGV 236 L +R G VA G D E ++ WD A +LVTEAGG+ + + Sbjct: 174 RLLPLVRGVRRPGAAALDLAYVACGRYDAFYEEALNPWDTAAGMLLVTEAGGRVSRVDTE 233 Query: 237 D-GPHGGDAVATNGILHDETLDRL 259 P D +ATNG +H++ + L Sbjct: 234 SYRPGDPDILATNGTIHEKASEML 257 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: 165 Number of extensions: 7 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 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 09 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