Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_041098372.1 SUTH_RS07950 inositol monophosphatase family protein
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000828635.1:WP_041098372.1 Length = 268 Score = 86.7 bits (213), Expect = 5e-22 Identities = 74/239 (30%), Positives = 117/239 (48%), Gaps = 21/239 (8%) Query: 8 LALALELAELADSITLDR--FEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADS 65 L +A++ A A I ++R + L + K V++ D A E A+ + + A PA Sbjct: 5 LNIAVKAARRAGQI-INRASMDVDKLRIDVKQQSDYVTEVDRAAEAAILDVLREAYPAYG 63 Query: 66 ILGEEFG--GDVEFSGRQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALA 123 IL EE G G S QWIIDP+DGT N++ G+P +A I L G V+ P Sbjct: 64 ILAEESGLAGTSPDSEYQWIIDPLDGTTNFIHGMPQYAISIGLAHKGVMTQAVVYDPNRN 123 Query: 124 RRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLSFSSLSGWAER--DLRDQFVSL-- 179 + AS+G GA+ + +++ V++ +KLD+A + +G+ R D D ++++ Sbjct: 124 EIFTASKGGGAY-----LNEKRIRVAKRTKLDEALIG----TGFPYRMFDHIDAYLAIFR 174 Query: 180 ---TDTTWRLRGYGDFFSYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGGKFTSLAG 235 T R VA G +D E +S WD+A ++L+TEAGG L+G Sbjct: 175 EVAQKTAGMRRPGAASLDLAWVACGRMDGFWELGLSPWDMAAGTLLITEAGGLVGDLSG 233 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: 140 Number of extensions: 7 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: 268 Length adjustment: 25 Effective length of query: 235 Effective length of database: 243 Effective search space: 57105 Effective search space used: 57105 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