Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate 3608266 Dshi_1670 glycosyl transferase family 3 (RefSeq)
Query= curated2:Q1AU89 (342 letters) >FitnessBrowser__Dino:3608266 Length = 323 Score = 86.3 bits (212), Expect = 1e-21 Identities = 67/217 (30%), Positives = 100/217 (46%), Gaps = 4/217 (1%) Query: 7 RKAAAGEPLSEGEAERALETIMEGGASPEATAALLTALRVRGESVQEIVGFARAMRRFAA 66 R PL+E EA A+ +++G + EA ALL LR+RGE+ EI GFA A+R Sbjct: 12 RGPGRARPLTETEARAAMGHVLDGTGAAEAVGALLMTLRLRGETEDEITGFAGALRDHMQ 71 Query: 67 RVRAPEGVVD-TCGTGGDAKGTINVSTAAAFVARGAGVVIAKHGNRAATSRAGSADVLEA 125 R RA + +D + G +G +A VA+ AG + HG A L A Sbjct: 72 RWRALDVDLDWPSYSAGRTRGLPWYLLSARLVAQ-AGYRVMLHGRNGGD--AALRSYLAA 128 Query: 126 LGAAIELSPEQVSRCIEEAGIGFMFARTHHPAMRHVAPVRAELPFRTVFNLLGPLTNPAG 185 G AI +P + ++ +G+ ++ + +RA L R+ N + NPAG Sbjct: 129 QGVAIAQTPAAATAALDASGLVYIPLEALSRRTTDLLALRAHLGLRSCVNTCLRVANPAG 188 Query: 186 ARRQLVGVFSAGYVRPMAEALEGLGAERALVVHGRDG 222 AR + GVF Y A + LG A+++ G G Sbjct: 189 ARVTVQGVFHPPYRALQETACKRLGDTAAMIIKGGGG 225 Lambda K H 0.317 0.134 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: 235 Number of extensions: 8 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: 342 Length of database: 323 Length adjustment: 28 Effective length of query: 314 Effective length of database: 295 Effective search space: 92630 Effective search space used: 92630 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