Align Phosphoglycerate mutase family protein, putative (characterized, see rationale)
to candidate NP_349347.1 CA_C2741 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Query= uniprot:N9V397 (205 letters) >NCBI__GCF_000008765.1:NP_349347.1 Length = 243 Score = 59.3 bits (142), Expect = 6e-14 Identities = 36/110 (32%), Positives = 58/110 (52%), Gaps = 5/110 (4%) Query: 1 MTKLILIRHGETEWNLLGKIQGCTDIELTPNGIQQANEVAQQIKGN---FDIIYSSPLHR 57 M KL+L+RHG++EWN + G TD++L+ +G+ +A + + +K N FD Y+S L R Sbjct: 1 MRKLVLLRHGQSEWNKENRFTGWTDVDLSVDGVSEAAQAGRILKKNNYTFDAAYTSVLKR 60 Query: 58 ALITAQKIAGDKEVHLIEGMKEIPFGTWEGHTFEELNGDINYKKFLSGED 107 A+ T Q + + ++ I K + LN D K+ GED Sbjct: 61 AIRTLQIVLYEMDLLWIPVYKSWKLNERHYGALQGLNKDETRDKY--GED 108 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: 135 Number of extensions: 7 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: 243 Length adjustment: 22 Effective length of query: 183 Effective length of database: 221 Effective search space: 40443 Effective search space used: 40443 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: 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