Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate HSERO_RS03050 HSERO_RS03050 hydrolase
Query= SwissProt::Q72H00 (249 letters) >FitnessBrowser__HerbieS:HSERO_RS03050 Length = 244 Score = 77.4 bits (189), Expect = 2e-19 Identities = 76/253 (30%), Positives = 109/253 (43%), Gaps = 45/253 (17%) Query: 1 MKLLLLDLDDTLLQDLPV---SRAVLEDLGRK----AGVEGFFARVKARAEALFREAPFY 53 ++ +L DLDDTL PV + +L D R+ A ++ R AL + P Y Sbjct: 17 IQAVLFDLDDTLWAIEPVLVRAETLLYDWLRQHAPAVAAAHTIASLRERRMALMQTDPAY 76 Query: 54 P---WAEAIGHSALEALWARYSTPGLEALAAWAGPFRERVFREALEEAGGAPERARELAE 110 W + H+AL + FRE AL + A Sbjct: 77 RINLWK--LRHTALSEV------------------FREHDVDLALVDPAMA--------- 107 Query: 111 AFFRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSLVLISG 170 F R L+ + E L + + L L ++NG DL+R GLA HF + + + Sbjct: 108 LFSEARSTVALFDDVEPALLRLKGK-LTLGSVSNGFADLER-----IGLAGHFGVSIAAH 161 Query: 171 EVGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPEDPE 230 G KPDP +F A A VAP VGD+P DV+GA+ AG++AVW++R R + Sbjct: 162 RFGRAKPDPAIFHAACEALQVAPGATVYVGDDPLLDVQGAQQAGLKAVWMNRFGRVLPED 221 Query: 231 ASPDLRVGDLREV 243 PD DL E+ Sbjct: 222 IRPDAVCRDLHEL 234 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: 152 Number of extensions: 8 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: 244 Length adjustment: 24 Effective length of query: 225 Effective length of database: 220 Effective search space: 49500 Effective search space used: 49500 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