Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate PP_5231 PP_5231 putative (S)-2-haloacid dehalogenase
Query= SwissProt::Q72H00 (249 letters) >FitnessBrowser__Putida:PP_5231 Length = 231 Score = 93.6 bits (231), Expect = 3e-24 Identities = 81/256 (31%), Positives = 117/256 (45%), Gaps = 48/256 (18%) Query: 1 MKLLLLDLDDTLLQDLPVSRAVLEDLGRKAGVEGFFARVKARAEALFREAPFYPWAEA-- 58 +KL+ DLDDTL PV A AE + R+ W EA Sbjct: 3 IKLITFDLDDTLWDTAPVI---------------------ATAEVVLRD-----WLEANA 36 Query: 59 --IGHSALEALWAR-----YSTPGLEALAAWAGPFRERVFREALEEAGGAPERARELA-- 109 +G +E L+A + PGL+ + R RV ALEE G + + A+ LA Sbjct: 37 PTLGSVPVEHLFAIRERLVQAEPGLKHRIS---ALRRRVLFHALEEVGYSEQHAQALANE 93 Query: 110 --EAFFRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSLVL 167 E F R + ++PE + L E R L ++TNG D+ R GLA +F L Sbjct: 94 GFEVFLHARHQVEIFPEVQPVL-EILRHQYILGVVTNGNADVSR-----LGLADYFRFAL 147 Query: 168 ISGEVGIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPE 227 + ++GIGKPDP F AL V A +GD+P D+ GA+ AG+RAVW + + Sbjct: 148 CAEDLGIGKPDPAPFLEALRRGEVDAGAAVHIGDHPGDDIAGAQRAGLRAVWFNPQGKAW 207 Query: 228 DPEASPDLRVGDLREV 243 + +PD + L ++ Sbjct: 208 TGDQAPDAEIQRLSQL 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: 139 Number of extensions: 9 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: 231 Length adjustment: 23 Effective length of query: 226 Effective length of database: 208 Effective search space: 47008 Effective search space used: 47008 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