Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate PP_3997 PP_3997 putative Glycosyl transferase
Query= curated2:Q1IZP8 (351 letters) >FitnessBrowser__Putida:PP_3997 Length = 333 Score = 69.7 bits (169), Expect = 1e-16 Identities = 62/210 (29%), Positives = 97/210 (46%), Gaps = 6/210 (2%) Query: 26 LTQAEAAAFMHEVMEGNVSGVRLAAALAALRVRGETPEEIAGFAQAMRASAVRVQVAPRE 85 LT+ EA A M ++EG V +L A L LR + E+ EE+AGF +A+RA ++A Sbjct: 34 LTREEARAAMTLLLEGKVEDTQLGAFLMLLRHKEESAEELAGFTEALRAHLQAPRIA--- 90 Query: 86 VLLDVVGTGGDGAHTFNISTTTAFVVAAAGVPVAKHGNRA-ASSRAGSADVLEALGVNLD 144 V LD G H A +A GV + HG A + R + +L+ L + L Sbjct: 91 VDLDWPTYAGKKRH-LPWYLLAAKCLANNGVRILMHGGGAHTAGRMYTEQLLDLLQIPLC 149 Query: 145 APPQLVADGVNELGIGFMFARNYHPALRHAAPVRADLAARTVFNILGPLANPAGASHLVV 204 V + +++ + F ++ P L+ +R L R+ + L + NP GA + Sbjct: 150 RDWAAVGNALDQHQLAFFPLHDWAPQLQRMIDLRNTLGLRSPIHSLARVLNPLGARCGLQ 209 Query: 205 GVYRPELTRMLAEVLRLLGAKGATVVYGSG 234 ++ P + E RLLG A V+ G G Sbjct: 210 SIFHPGYQAVHREASRLLG-DHAVVIKGDG 238 Lambda K H 0.318 0.131 0.375 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: 241 Number of extensions: 12 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: 351 Length of database: 333 Length adjustment: 29 Effective length of query: 322 Effective length of database: 304 Effective search space: 97888 Effective search space used: 97888 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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