Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate 6936246 Sama_0435 putative phosphoglycerate mutase family protein (RefSeq)
Query= SwissProt::F4KI56 (238 letters) >FitnessBrowser__SB2B:6936246 Length = 193 Score = 60.8 bits (146), Expect = 2e-14 Identities = 54/162 (33%), Positives = 78/162 (48%), Gaps = 21/162 (12%) Query: 25 TEIVLVRHGETTWNAAGRIQGQIESDLNEVGLKQAVAIAERLGK--EERPVAVYSSDLKR 82 T+I L+RHG+T +NA R+QG +S L +G +QA A + L + + A+ +S L R Sbjct: 3 TDIFLLRHGQTEFNAQRRLQGHCDSPLTLLGREQARAYGQALKRCGDLDDYALIASPLGR 62 Query: 83 AKDTALMIAKTCFCPEVIEVPDLKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLE-I 141 A +TA ++A+T +PD + + G E E E SS LE I Sbjct: 63 AMETAAIVAQTLGRDPESVIPDQRVKEAGL---------GEWEQEHIPDIHSSWPGLEAI 113 Query: 142 PG------GGESFDQLADRSMDALEQIAKKHKGERVIVVTHG 177 PG G E L +R + LE A K VI+V+HG Sbjct: 114 PGWYIKGPGAEPLSALRERLLHWLEDPATPQK---VILVSHG 152 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: 114 Number of extensions: 6 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: 238 Length of database: 193 Length adjustment: 22 Effective length of query: 216 Effective length of database: 171 Effective search space: 36936 Effective search space used: 36936 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: 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