Align Putative phosphoserine phosphatase 2; PSP 2; PSPase 2; Metal-independent phosphoserine phosphatase 2; iPSP2; O-phosphoserine phosphohydrolase 2; EC 3.1.3.3 (characterized)
to candidate 14775 b0638 predicted alpha-ribazole-5'-P phosphatase (NCBI)
Query= SwissProt::D3DFP8 (203 letters) >FitnessBrowser__Keio:14775 Length = 203 Score = 94.7 bits (234), Expect = 1e-24 Identities = 61/196 (31%), Positives = 103/196 (52%), Gaps = 7/196 (3%) Query: 3 RLYLVRHAQSEYNEKGIFQGRLDSDLTPLGFVQARLLAREFLKKKVDIIYSSPQRRAYKT 62 RL+L+RH +++ N G++ G + LT G QA+ L D++ S RA T Sbjct: 2 RLWLIRHGETQANIDGLYSGHAPTPLTARGIEQAQNLHTLLHGVSFDLVLCSELERAQHT 61 Query: 63 A-LTISD-MLGTQLVVDERLREMSFGEYEGKHFWSMLEAHKDVFLNWLSNPVKHPLPTQ- 119 A L +SD L Q++ + L EM FG++E +H +++ + + W N +H +PT Sbjct: 62 ARLVLSDRQLPVQIIPE--LNEMFFGDWEMRHHRDLMQEDAENYSAW-CNDWQHAIPTNG 118 Query: 120 ESMEEFEKRVRSFLEDVKS-SHYQNMLIVAHGGTLHAIVCLLTGIGLENLWNIHMDNAGI 178 E + F +RV F+ + HYQN+L+V+H G L ++ L G+ E +W+ +D Sbjct: 119 EGFQAFSQRVERFIARLSEFQHYQNILVVSHQGVLSLLIARLIGMPAEAMWHFRVDQGCW 178 Query: 179 TEIHMEGEKSTLVYLN 194 + I + + +TL LN Sbjct: 179 SAIDINQKFATLRVLN 194 Lambda K H 0.321 0.136 0.402 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: 121 Number of extensions: 7 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: 203 Length of database: 203 Length adjustment: 21 Effective length of query: 182 Effective length of database: 182 Effective search space: 33124 Effective search space used: 33124 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: 45 (21.9 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