Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate GFF2329 Psest_2377 Anthranilate phosphoribosyltransferase
Query= curated2:B8GJ30 (339 letters) >FitnessBrowser__psRCH2:GFF2329 Length = 327 Score = 77.4 bits (189), Expect = 5e-19 Identities = 66/215 (30%), Positives = 98/215 (45%), Gaps = 11/215 (5%) Query: 13 QDLPEQMAAGAMEAIMTGAATNAQIGSFLTALRMKGESPAEVAAFAAVMR--VHAVQFQV 70 +DL + A AM ++ G +AQ+G+FL LR K ES E+A F +R V A V Sbjct: 26 RDLTREEAREAMGMLLDGKVEDAQLGAFLMLLRHKEESAEELAGFTEAVRARVQAPAISV 85 Query: 71 RGGQGRLVDTCGTGGDQAGTFNISTAAAIVAAGAGVRIVKHGNRS-ASGRCGSADVLEEL 129 +D G + AA +AA GVRI+ HG + +GR + LE L Sbjct: 86 D------IDWPSYAGKKRHLPWYLLAAKCLAAN-GVRILMHGGGAHTAGRIYTEQQLELL 138 Query: 130 GVNLAMTPAQEQATLEQAGIVFLFAQTHHPAMKHVAAARKEIGIRTVFNILGPLTNPAGA 189 G+ Q A L+Q+ + F+ P ++ + R +G+R+ + L L NP GA Sbjct: 139 GIRRCENWQQVSAALDQSNLAFIPLGAWMPVLQRMIDMRNLLGLRSPVHSLARLLNPLGA 198 Query: 190 DAQLLGVPEPSLLDLLPPVLQTLGVDHAMIVCGGG 224 L + P D LG DHA+++ G G Sbjct: 199 RCGLQSIFHPGYQDAHRQASTLLG-DHAIVIKGEG 232 Lambda K H 0.317 0.133 0.371 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: 227 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: 339 Length of database: 327 Length adjustment: 28 Effective length of query: 311 Effective length of database: 299 Effective search space: 92989 Effective search space used: 92989 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