Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate CCNA_00310 CCNA_00310 3'-phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase family protein
Query= curated2:P56160 (259 letters) >FitnessBrowser__Caulo:CCNA_00310 Length = 259 Score = 109 bits (273), Expect = 5e-29 Identities = 83/262 (31%), Positives = 129/262 (49%), Gaps = 16/262 (6%) Query: 4 DLQLALELAEKAGKLTLDYFGRRS-LQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDG 62 DL L + A +AG+L L R S L ++SK +PVT+AD + L+R + A+ PD G Sbjct: 3 DLDLIIAAAREAGELALG--ARESGLTIWSKEGGSPVTDADLAVDTLLRTELRAERPDYG 60 Query: 63 LFGEEFDEHPS--GNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALG 120 EE + P+ GR++++DPIDGT +F+ G P + V IA+ +G V++ PAL Sbjct: 61 WLSEETADDPARLATGRQFVVDPIDGTVAFMKGKPWFAVSIAVVEDGQPIAAVVHAPALD 120 Query: 121 ELYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAGLVRG 180 E Y A A +NG+P+ S + + + + P P +RI+ Sbjct: 121 ETYAATLQGPATLNGAPIAPSD-TDALEGAAMLGDAKMFAHPAWREPWPTMRIETRNSIA 179 Query: 181 WGDCYGHMLVASGRAEVAVD-KIMSPWDCAAVIPIVEEAGGCCFDYRGR-----QSIIDG 234 + C LVA+G + AV S WD AA I + AG D++GR + + Sbjct: 180 YRAC----LVAAGAFDAAVALSPKSEWDVAAADLICQRAGAALSDHKGRPYAYNRPVPQV 235 Query: 235 EGLVSANNAMGRNLIAAIGNGE 256 LV AN A+ ++ +G+ E Sbjct: 236 PSLVCANRALAPLILNRVGHIE 257 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: 169 Number of extensions: 8 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: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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