Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate GFF2329 Psest_2377 Anthranilate phosphoribosyltransferase
Query= curated2:B1I3Z8 (346 letters) >FitnessBrowser__psRCH2:GFF2329 Length = 327 Score = 73.2 bits (178), Expect = 9e-18 Identities = 65/215 (30%), Positives = 95/215 (44%), Gaps = 9/215 (4%) Query: 11 GGEDLEQHEAEAVMAEIMDGEATSAQIGALLAGLRLKKETAAEIRGFARAMRARAEQVPT 70 G DL + EA M ++DG+ AQ+GA L LR K+E+A E+ GF A+RAR + Sbjct: 24 GARDLTREEAREAMGMLLDGKVEDAQLGAFLMLLRHKEESAEELAGFTEAVRARVQAPAI 83 Query: 71 RHELVADTCGTGGDGAQTFNISTTAAFVVAGAGVPVAKHGNTA-VSSRCGSADVLRHLGV 129 ++ D G + AA +A GV + HG A + R + L LG+ Sbjct: 84 SVDI--DWPSYAGK-KRHLPWYLLAAKCLAANGVRILMHGGGAHTAGRIYTEQQLELLGI 140 Query: 130 NLDLTPAQMGACLDEVGIAFLFAPRLHRAMQHAAGPRKELGIRTVFNILGPLTNPVRPRV 189 Q+ A LD+ +AF+ +Q R LG+R+ + L L NP+ R Sbjct: 141 RRCENWQQVSAALDQSNLAFIPLGAWMPVLQRMIDMRNLLGLRSPVHSLARLLNPLGARC 200 Query: 190 QVLGVFDAAV--AELVADALAGLEVERAFVIHGAG 222 + +F A A L G + A VI G G Sbjct: 201 GLQSIFHPGYQDAHRQASTLLG---DHAIVIKGEG 232 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: 259 Number of extensions: 14 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: 327 Length adjustment: 28 Effective length of query: 318 Effective length of database: 299 Effective search space: 95082 Effective search space used: 95082 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 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