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 CCNA_01413 CCNA_01413 phosphoglycerate mutase family protein
Query= SwissProt::D3DFP8 (203 letters) >FitnessBrowser__Caulo:CCNA_01413 Length = 199 Score = 72.0 bits (175), Expect = 7e-18 Identities = 48/153 (31%), Positives = 82/153 (53%), Gaps = 9/153 (5%) Query: 4 LYLVRHAQSEYNEKGIFQGRLDSDLTPLGFVQARLLAR---EFLKKKVDI---IYSSPQR 57 +YL RH Q+ +N +G QGR +SDLTPLG +QA+ + + + ++++ + +SP R Sbjct: 2 IYLCRHGQTFHNREGRLQGRTESDLTPLGLLQAQAMGQLLGDLVRREPPAPWRLVASPLR 61 Query: 58 RAYKTALTISDMLGTQLVVDERLREMSFGEYEGKHFWSMLEAHKDVFLNWLSNPVKHPLP 117 RA +TA I + LG + DERL E+ GE+ G+ E H + + P Sbjct: 62 RARRTAEAIGEHLGLAVDFDERLVEIDVGEWSGR---LREEVHGENPHLVGDDAWGFQAP 118 Query: 118 TQESMEEFEKRVRSFLEDVKSSHYQNMLIVAHG 150 E+ E R+ S+L + + + +++V+HG Sbjct: 119 GGETYEAMMVRLTSWLSEQATEPERRLIVVSHG 151 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: 100 Number of extensions: 5 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: 199 Length adjustment: 21 Effective length of query: 182 Effective length of database: 178 Effective search space: 32396 Effective search space used: 32396 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