Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_027457796.1 K420_RS0109145 DNA-binding protein YbiB
Query= curated2:Q0RFI3 (369 letters) >NCBI__GCF_000519045.1:WP_027457796.1 Length = 329 Score = 71.6 bits (174), Expect = 3e-17 Identities = 66/221 (29%), Positives = 99/221 (44%), Gaps = 6/221 (2%) Query: 9 GALLARE-SLDSARTAWAMDQIMAGAATPAQIAGFAVALRAKGETPAEIGGLIAAMRAHA 67 GA AR+ + + AR +A ++ G ++ VALR KGE+ E+ G +AA Sbjct: 13 GAQGARDLTQEDARQLYAA--MLDGGVPDLELGAIIVALRVKGESLDEMLGFLAATDERT 70 Query: 68 APLRIPDEIRARAVDTCGTGGDRSNTVNLSTMAALVVAGAGVPVIKHGNRAASSACGSAD 127 PL +P R R V G R NL+ + AL++ GVPV+ HG SA Sbjct: 71 HPLEMPPG-RGRPVVLPTYNGARKEA-NLTPLLALLLQRFGVPVLVHGLIEGYGRVTSAH 128 Query: 128 LLAELGVAIDLPPAGVEACLRAAGIAFCFARIFHPAMRHVGGPRAEIGVPTAFNILGPLT 187 + ELGV P +A L G+AF P + ++ RA +GV + + L L Sbjct: 129 IFRELGVLPVASPHQAQAALDDKGLAFMPLSALCPGIHNLLSLRARMGVRNSAHSLVKLL 188 Query: 188 NPAEPGAQAVGVA-DARLAPVVAQVLADRGTRALVFRGDDG 227 +P A V A ++ ++ RG L+ RG +G Sbjct: 189 DPFHGDAVLVAPATHPDFIDLMRNIMLVRGQHGLLLRGTEG 229 Lambda K H 0.318 0.131 0.385 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: 275 Number of extensions: 15 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: 369 Length of database: 329 Length adjustment: 29 Effective length of query: 340 Effective length of database: 300 Effective search space: 102000 Effective search space used: 102000 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 10 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