Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate GFF5019 PS417_25715 anthranilate phosphoribosyltransferase
Query= SwissProt::P00904 (531 letters) >FitnessBrowser__WCS417:GFF5019 Length = 349 Score = 199 bits (506), Expect = 1e-55 Identities = 126/336 (37%), Positives = 181/336 (53%), Gaps = 6/336 (1%) Query: 200 LQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATAL 259 ++ L ++ LS E + ++ G+ Q+ A +++M+++ E +EI GA + + Sbjct: 3 IKTALSRIVGHLDLSTAEMSDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVM 62 Query: 260 LENAAPFPRPDYL-FADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGS 318 E A D+VGTGGDG+N N+STAS+FV AA G VAKHGNR+VS KSGS Sbjct: 63 RELADKVELKTLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGS 122 Query: 319 SDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGP 378 +DLL A GI L++ + + +D +G+ F+FA +H +HA R+ L RTLFN+LGP Sbjct: 123 ADLLEAAGIYLNLTPVQVARCIDSVGIGFMFAQSHHGAMKHAAGPRKDLGLRTLFNMLGP 182 Query: 379 LINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHS-GGMDEVSLHAPTIVAELHD 437 L NPA ++GV+S L P+AE L+ LG + VVHS G+DE SL APT VAEL + Sbjct: 183 LTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKN 242 Query: 438 GEIKSYQLTAEDFGLTPYHQEQLAGGTP----EENRDILTRLLQGKGDAAHEAAVAANVA 493 ++ Y + ED G+ LA +P E RD L R G A E V A Sbjct: 243 DQVTEYWVEPEDLGMKSQSLHGLAVESPAASLELIRDALGRRKTENGQKAAEMIVLNAGA 302 Query: 494 MLMRLHGHEDLQANAQTVLEVLRSGSAYDRVTALAA 529 L L+ + L +G A +++ L A Sbjct: 303 ALYAADHAYSLKEGVALAHDALHTGLAREKLEELGA 338 Score = 25.4 bits (54), Expect = 0.004 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 2/48 (4%) Query: 32 RNHIPAQTLIERLATMSNPVLMLSPGPGVPSEAGCMP--ELLTRLRGK 77 R + +TL L ++NP + GV S+A C P E+L RL K Sbjct: 168 RKDLGLRTLFNMLGPLTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSK 215 Lambda K H 0.318 0.134 0.388 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: 400 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 531 Length of database: 349 Length adjustment: 32 Effective length of query: 499 Effective length of database: 317 Effective search space: 158183 Effective search space used: 158183 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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