Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_013721332.1 ALIDE2_RS02755 histidine phosphatase family protein
Query= SwissProt::F4KI56 (238 letters) >NCBI__GCF_000204645.1:WP_013721332.1 Length = 215 Score = 120 bits (301), Expect = 2e-32 Identities = 74/206 (35%), Positives = 110/206 (53%), Gaps = 7/206 (3%) Query: 22 SEVTEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPVAVYSSDLK 81 ++ T I+ +RHGET WN RIQG ++ LN+ GL QA + + L +E A+YSSDL Sbjct: 2 NQATRIIAIRHGETAWNVDTRIQGHLDIPLNDTGLWQARQVGQALA-DEPVAAIYSSDLL 60 Query: 82 RAKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLEI 141 RA TA +A+ P E L+ER GS QG +++ + PE + D Sbjct: 61 RAWATAQAVAQATGAPLNPE-RGLRERSFGSFQGRTFEQIEREVPEQALRWRKRDPDFAP 119 Query: 142 PGGGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIYLRIT----QASSAGKLL 197 GGGES L +R + QIA +H G+++++V HGGV+ +Y T QA +L Sbjct: 120 DGGGESLTMLRERIACTVHQIAARHSGQQIVLVAHGGVMDVLYRLATHLDLQAPRTWQLT 179 Query: 198 NASVN-VVHLRDQKWIIDSWSDVSHL 222 NA++N ++ D + W+D HL Sbjct: 180 NAAINRLLWTGDHGLALVGWADTQHL 205 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: 171 Number of extensions: 18 Number of successful extensions: 3 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: 215 Length adjustment: 22 Effective length of query: 216 Effective length of database: 193 Effective search space: 41688 Effective search space used: 41688 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 10 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