Align Phosphoglycerate mutase (characterized, see rationale)
to candidate WP_085218187.1 B9N75_RS07190 2,3-diphosphoglycerate-dependent phosphoglycerate mutase
Query= uniprot:A0A0H2XA29 (214 letters) >NCBI__GCF_900177405.1:WP_085218187.1 Length = 228 Score = 49.7 bits (117), Expect = 4e-11 Identities = 36/126 (28%), Positives = 56/126 (44%), Gaps = 8/126 (6%) Query: 3 ILLARHGETPWNAEGRYQGQIDIPLSPVGEGQGAALGARLQALQITRAVASPLSRAQATA 62 ++L RHG++ WN E R+ G D+ L+P GE + A G L + + + +A Sbjct: 4 LVLIRHGQSAWNLENRFTGWWDVNLTPQGEAEAKAAGELLAERGLDFDICFTSLQTRAIK 63 Query: 63 TLALGSARAGLLQTDAD----LQEIAHGEWEGLLASEINDKDPA-RLRAWREE---PDTV 114 TL + G L + L E +G GL +E K A ++ WR P Sbjct: 64 TLNIALEAMGRLWLPVEKHWRLNERHYGGLTGLDKAETAAKHSAEQVHIWRRSFDIPPPA 123 Query: 115 LMPGGE 120 + PGG+ Sbjct: 124 MEPGGD 129 Lambda K H 0.319 0.135 0.409 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: 136 Number of extensions: 9 Number of successful extensions: 1 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: 214 Length of database: 228 Length adjustment: 22 Effective length of query: 192 Effective length of database: 206 Effective search space: 39552 Effective search space used: 39552 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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