Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate 3607790 Dshi_1199 Inositol-phosphate phosphatase (RefSeq)
Query= curated2:P56160 (259 letters) >FitnessBrowser__Dino:3607790 Length = 264 Score = 119 bits (298), Expect = 6e-32 Identities = 86/257 (33%), Positives = 132/257 (51%), Gaps = 10/257 (3%) Query: 4 DLQLALELAEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDG 62 +L + ++ A AG+ L D+ +LQ K V+ AD A+E++ + P+ G Sbjct: 7 NLNVMIKAARAAGRSLVKDFREVENLQSSMKGAGDFVSRADLRAQEILENELREARPNYG 66 Query: 63 LFGEEFDEHPSGNG--RRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALG 120 EE E G RRWI+DP+DGT +F+HG+P + V I LE +G + GV+ PA Sbjct: 67 WLAEEAKEEVIGKDPTRRWIVDPLDGTTNFLHGMPHWAVSIGLEHKGDVVAGVVFDPAKD 126 Query: 121 ELYQAERGSGAFMNGSPVQVSA----IAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAG 176 E++ AE+G GA+MN + ++VS I A+ + F YL P + + QL Sbjct: 127 EMFFAEKGQGAWMNQTRMRVSGRRMMIESVFATGLPFANNAYL--PATLKDLGQLLPQCA 184 Query: 177 LVRGWGDCYGHM-LVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGE 235 VR WG + VA+GR E ++ + PWD AA I +V EAGG R Q +++ Sbjct: 185 GVRRWGAAALDLAYVAAGRYEGYWERGLKPWDLAAGIVLVREAGGLVEPIREDQLLLEDG 244 Query: 236 GLVSANNAMGRNLIAAI 252 +++A+ M A I Sbjct: 245 HILAASEPMFGKFAATI 261 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: 167 Number of extensions: 8 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: 259 Length of database: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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 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