Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate WP_066918409.1 ACG33_RS02460 2,3-diphosphoglycerate-dependent phosphoglycerate mutase
Query= SwissProt::F4KI56 (238 letters) >NCBI__GCF_001579945.1:WP_066918409.1 Length = 250 Score = 52.4 bits (124), Expect = 8e-12 Identities = 58/192 (30%), Positives = 85/192 (44%), Gaps = 39/192 (20%) Query: 26 EIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGKEERPV--AVYSSDLKRA 83 ++VL+RHG++TWN G ++ DL + GL +A A A RL K E ++S LKRA Sbjct: 4 KLVLIRHGQSTWNLENLFTGWVDVDLTDQGLAEARA-AGRLLKTEGFAFDLAFTSVLKRA 62 Query: 84 KDTALMIAKTCFCPEVIEVP-----DLKERHVGSLQGL-----YWKEGAEK--------- 124 T +I +++ +P L ERH G+LQGL K GAE+ Sbjct: 63 IRTLWVILDEM---DLMWLPVERSWRLNERHYGALQGLDKAQTVHKHGAEQVKLWRRSYD 119 Query: 125 ---------EPE--AYSAFFSSQNDLEIPGGGESFDQLADRSMDALEQ--IAKKHKGERV 171 +P + ++S E+P ES DR + + G V Sbjct: 120 VPPPPLPIDDPRHPRFERRYASLPPQELP-AAESLKTTLDRVLPYWNSRLAPELAAGRNV 178 Query: 172 IVVTHGGVLRAI 183 +VV HG LRA+ Sbjct: 179 LVVAHGNSLRAL 190 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: 157 Number of extensions: 5 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 238 Length of database: 250 Length adjustment: 24 Effective length of query: 214 Effective length of database: 226 Effective search space: 48364 Effective search space used: 48364 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