Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_085635951.1 MGEO_RS06670 glycosyl transferase family protein
Query= curated2:B1I3Z8 (346 letters) >NCBI__GCF_002115805.1:WP_085635951.1 Length = 316 Score = 76.3 bits (186), Expect = 1e-18 Identities = 66/208 (31%), Positives = 92/208 (44%), Gaps = 5/208 (2%) Query: 15 LEQHEAEAVMAEIMDGEATSAQIGALLAGLRLKKETAAEIRGFARAMRARAEQVPTRHEL 74 L + EA M ++ A A IGALL LR+K ETA EI GFA+A + +P ++ Sbjct: 20 LTRDEARDAMRSMLSEGAEPAAIGALLMLLRMKGETAEEIAGFAQAAQEWGPDLP---QV 76 Query: 75 VADTCGTGGDGAQTFNISTTAAFVVAGAGVPVAKHGNTAVSSRCGSADVLRHLGVNLDLT 134 D + +A +VA AG V HG + + L G+ + T Sbjct: 77 DLDWPSYAAGRTRGHPWFLLSAKLVAEAGHTVLLHGFNGPDAAVRNG--LTDAGIGIADT 134 Query: 135 PAQMGACLDEVGIAFLFAPRLHRAMQHAAGPRKELGIRTVFNILGPLTNPVRPRVQVLGV 194 PA + L + IA+L + H + R LG+R+ N + + NP R R V GV Sbjct: 135 PATLSRLLAQDRIAYLPLEQWHPRLFDLLRLRDVLGLRSCINTICRMLNPARARASVQGV 194 Query: 195 FDAAVAELVADALAGLEVERAFVIHGAG 222 F + L ADA L E VI G G Sbjct: 195 FHPSYRLLQADAATQLGWESLSVIKGGG 222 Lambda K H 0.319 0.135 0.384 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: 249 Number of extensions: 16 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: 346 Length of database: 316 Length adjustment: 28 Effective length of query: 318 Effective length of database: 288 Effective search space: 91584 Effective search space used: 91584 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: 49 (23.5 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