Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate H281DRAFT_05713 H281DRAFT_05713 anthranilate phosphoribosyltransferase
Query= SwissProt::P00904 (531 letters) >FitnessBrowser__Burk376:H281DRAFT_05713 Length = 343 Score = 222 bits (565), Expect = 2e-62 Identities = 129/331 (38%), Positives = 184/331 (55%), Gaps = 2/331 (0%) Query: 199 TLQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATA 258 T Q L++ + + + E L ++RGEL P AA + ++++ E EI AAT Sbjct: 4 TPQEALQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAAATV 63 Query: 259 LLENAAPFPRPDYL-FADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSG 317 + E A D F DIVGTGGDGS++ NISTA+ FV+AA G KVAKHGNR VSSKSG Sbjct: 64 MREFARHVEVQDNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSSKSG 123 Query: 318 SSDLLAAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLG 377 S+D+L A G+N+D+ ++ ++ E G+ F+FAP +H ++ PVR++L RT+FN+LG Sbjct: 124 SADVLEALGVNIDLQPEQVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFNILG 183 Query: 378 PLINPAHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVHS-GGMDEVSLHAPTIVAELH 436 PL NPA P L+GV+ +LV ++ LG + VV+ GMDEVSL A T V EL Sbjct: 184 PLTNPAGAPNQLMGVFHADLVGIQVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVGELR 243 Query: 437 DGEIKSYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKGDAAHEAAVAANVAMLM 496 DGE++ Y++ EDFG+ L E++ +L L K A E L Sbjct: 244 DGEVREYEIHPEDFGMQMVSNRTLKVADATESKAMLLEALDNKPGVAREIVTLNAGTALY 303 Query: 497 RLHGHEDLQANAQTVLEVLRSGSAYDRVTAL 527 + + + E + SG A +V L Sbjct: 304 SANVASSIANGIELAREAIASGKARAKVDEL 334 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: 435 Number of extensions: 18 Number of successful extensions: 3 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: 531 Length of database: 343 Length adjustment: 32 Effective length of query: 499 Effective length of database: 311 Effective search space: 155189 Effective search space used: 155189 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