Align Phosphoglycerate mutase family protein, putative (characterized, see rationale)
to candidate WP_007472917.1 CMTB2_RS00400 2,3-diphosphoglycerate-dependent phosphoglycerate mutase
Query= uniprot:N9V397 (205 letters) >NCBI__GCF_000170735.1:WP_007472917.1 Length = 229 Score = 69.7 bits (169), Expect = 4e-17 Identities = 38/111 (34%), Positives = 64/111 (57%), Gaps = 8/111 (7%) Query: 1 MTKLILIRHGETEWNLLGKIQGCTDIELTPNGIQQANEVAQQIKG---NFDIIYSSPLHR 57 M KL+L+RHG++EWN + G D++L P GI++A + Q++K +FDI +SS L R Sbjct: 1 MAKLVLVRHGKSEWNKQNRFTGWVDVDLAPEGIEEAKKAGQKLKSAGLSFDICFSSYLKR 60 Query: 58 ALITAQKIAGDKEVHLIEGMK-----EIPFGTWEGHTFEELNGDINYKKFL 103 A+ T I + ++ I+ +K E +G G +E+ ++ +KFL Sbjct: 61 AIKTGIIILEELDLLWIDHLKDWRFNERHYGALTGLNKDEVKAEVGEEKFL 111 Lambda K H 0.318 0.135 0.410 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: 158 Number of extensions: 11 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: 205 Length of database: 229 Length adjustment: 22 Effective length of query: 183 Effective length of database: 207 Effective search space: 37881 Effective search space used: 37881 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 (21.7 bits) S2: 45 (21.9 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