Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_012169029.1 AZC_RS02530 inositol monophosphatase family protein
Query= curated2:P56160 (259 letters) >NCBI__GCF_000010525.1:WP_012169029.1 Length = 262 Score = 109 bits (272), Expect = 7e-29 Identities = 80/253 (31%), Positives = 123/253 (48%), Gaps = 7/253 (2%) Query: 2 TPDLQLALELAEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPD 60 +P + + ++ KAG+ L D+ +LQV K V+ ADR AEE + +S P Sbjct: 4 SPLITVMVQAVRKAGRNLARDFGEVENLQVSLKGPANFVSSADRKAEETLYAELSRARPG 63 Query: 61 DGLFGEEFDE-HPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPAL 119 G EE + W+IDP+DGT +F+HG+PL+ + +AL G GVI P Sbjct: 64 YGFTMEERGKVEGQDEANEWVIDPLDGTTNFLHGIPLFAISVALVRNGVPFAGVIFNPVT 123 Query: 120 GELYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAGLVR 179 ELY AE+G GA++N ++V+A A VV +L N +L + G V Sbjct: 124 DELYVAEKGQGAYLNDRRLRVAA-RRKLADCVVGCGIPHLGRGDHNKFQRELALVQGQVA 182 Query: 180 GWGDCYGHML----VASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGE 235 G L VA+GR + ++ +S WD AA + ++ EAGG D G ++ Sbjct: 183 GVRRTGAAALDLAWVAAGRFDAFWERDLSSWDMAAGMILIREAGGSVTDLDGHDKSLENG 242 Query: 236 GLVSANNAMGRNL 248 +++ N M +L Sbjct: 243 HIIAGNADMREDL 255 Lambda K H 0.319 0.138 0.415 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: 179 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: 259 Length of database: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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