Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_041097122.1 SUTH_RS03500 histidine phosphatase family protein
Query= SwissProt::F4KI56 (238 letters) >NCBI__GCF_000828635.1:WP_041097122.1 Length = 214 Score = 120 bits (302), Expect = 2e-32 Identities = 82/208 (39%), Positives = 105/208 (50%), Gaps = 7/208 (3%) Query: 22 SEVTEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPVAVYSSDLK 81 + +T VRHGET WN RIQGQI+ DLN G QA A+ L K A YSSDL Sbjct: 4 ARITRFCFVRHGETDWNGEKRIQGQIDIDLNAAGEAQARAVGVGLAKHSF-AAAYSSDLL 62 Query: 82 RAKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEI 141 RA TA IA V P L+ER+ G LQG+ +E + + PEA+ + D Sbjct: 63 RAWRTA-QIATRGLGLAVSPAPTLRERNFGVLQGITVQEASVQRPEAHRHHQARTPDYNY 121 Query: 142 PGGGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYL----RITQASSAGKLL 197 GES A R LE +A +H G+ V+ THGGVL +Y R +L Sbjct: 122 E-SGESLIAFAARVATGLEAMAARHVGQSVLAFTHGGVLDVVYRAAAGRALDVPRDFQLP 180 Query: 198 NASVNVVHLRDQKWIIDSWSDVSHLSSV 225 NA+ N + D+ W + SW+D SHL V Sbjct: 181 NAAFNWLEYDDKGWRLISWADCSHLQRV 208 Lambda K H 0.315 0.132 0.387 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: 166 Number of extensions: 9 Number of successful extensions: 4 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: 238 Length of database: 214 Length adjustment: 22 Effective length of query: 216 Effective length of database: 192 Effective search space: 41472 Effective search space used: 41472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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