Align Phosphoribosyl-ATP pyrophosphatase; PRA-PH; EC 3.6.1.31 (uncharacterized)
to candidate WP_037568880.1 BS73_RS02710 LacI family transcriptional regulator
Query= curated2:C5CBJ9 (87 letters) >NCBI__GCF_000744815.1:WP_037568880.1 Length = 334 Score = 32.7 bits (73), Expect = 3e-06 Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 11/92 (11%) Query: 3 TFDELYAELTRKVQERPEGSGTVAQIDAGVHAI-------GKKVVEEAAEVWMAAEYESD 55 TF+ LTR ++ERPE SG V Q +A + + G+ V E+A+ V + E + Sbjct: 222 TFESTAGVLTRILEERPETSGFVVQNEAAIRPLLTLLRQFGRVVPEDASVVAICPESVAL 281 Query: 56 EAAAEEISQLLYHVQTMMIARGISLEDVYRHL 87 +++ + S + + RG +LE V HL Sbjct: 282 QSSPQLTS---VSIPAERMGRG-ALELVMAHL 309 Lambda K H 0.314 0.128 0.348 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: 48 Number of extensions: 1 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: 87 Length of database: 334 Length adjustment: 18 Effective length of query: 69 Effective length of database: 316 Effective search space: 21804 Effective search space used: 21804 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 43 (21.2 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