Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate Pf1N1B4_2170 Putative FMN hydrolase (EC 3.1.3.-); 5-Amino-6-(5'-phosphoribitylamino)uracil phosphatase
Query= SwissProt::Q72H00 (249 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2170 Length = 233 Score = 103 bits (257), Expect = 3e-27 Identities = 82/252 (32%), Positives = 117/252 (46%), Gaps = 40/252 (15%) Query: 1 MKLLLLDLDDTLLQDLPVSRAVLEDLGRKAGVEGFFARVKARAEALFREAPFYPWAEAIG 60 ++L+ DLDDTL PV A AE + RE A +G Sbjct: 3 IQLITFDLDDTLWDTAPVI---------------------ASAEVILREW-LTEHAPNLG 40 Query: 61 HSALEALWA-----RYSTPGLEALAAWAGPFRERVFREALEEAGGAPERARELA----EA 111 +E LW+ S P L+ + R RV ALEEAG A +LA E Sbjct: 41 AVPVEHLWSIRERVLSSEPNLKHRIS---ALRRRVLFHALEEAGYGHIEASDLADQGFEV 97 Query: 112 FFRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSLVLISGE 171 F R + ++PE E L E + AL ++TNG D++R GLA +F L + + Sbjct: 98 FLHARHQIEVFPEVEPTL-ETLAKHYALGVVTNGNADVRR-----LGLADYFKFALCAED 151 Query: 172 VGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPEDPEA 231 +GI KPD RLF AL G E A +GD+P D+ GA+ AG+RA+W + + + + Sbjct: 152 IGIAKPDARLFHEALQRGGATAETAVHIGDHPGDDIAGAQQAGLRAIWFNPAGKVWEAQT 211 Query: 232 SPDLRVGDLREV 243 +PD + L E+ Sbjct: 212 APDAEIRSLNEL 223 Lambda K H 0.322 0.140 0.417 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: 142 Number of extensions: 6 Number of successful extensions: 1 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: 249 Length of database: 233 Length adjustment: 23 Effective length of query: 226 Effective length of database: 210 Effective search space: 47460 Effective search space used: 47460 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 (21.9 bits) S2: 46 (22.3 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