Align Bifunctional protein TrpGD; EC 4.1.3.27; EC 2.4.2.18 (characterized)
to candidate 209403 DVU0467 anthranilate phosphoribosyltransferase
Query= SwissProt::P00904 (531 letters) >MicrobesOnline__882:209403 Length = 332 Score = 204 bits (520), Expect = 3e-57 Identities = 122/302 (40%), Positives = 170/302 (56%), Gaps = 2/302 (0%) Query: 203 ILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHPNEIAGAATALLEN 262 ILE L L + + F++++ G++ P Q + L+ ++++GE +E+ A A L Sbjct: 7 ILETLATGCDLHPEMAGAGFASLMDGDMTPAQAGSFLMGLRMKGETADEMTEAVRAALAR 66 Query: 263 AAPFPRPDYLFADIVGTGGDGSNSINISTASAFVAAACGLKVAKHGNRSVSSKSGSSDLL 322 A D DIVGTGGDG +S N STA+A A G KV KHGNR+VSS GS+D + Sbjct: 67 AVTVRGVDAPSIDIVGTGGDGRSSFNCSTATALTLAGMGHKVVKHGNRAVSSSCGSADAI 126 Query: 323 AAFGINLDMNADKSRQALDELGVCFLFAPKYHTGFRHAMPVRQQLKTRTLFNVLGPLINP 382 G+ L+++A L E G FLFAP++H FRH MP+R++L RTLFN+LGPL+NP Sbjct: 127 EGLGLPLEVDAADVPAMLHERGFAFLFAPRFHPAFRHVMPIRRELGVRTLFNLLGPLLNP 186 Query: 383 AHPPLALIGVYSPELVLPIAETLRVLGYQRAAVVH-SGGMDEVSLHAPTIVAELHDGEIK 441 A P L+GV L+ +AETLR G RAAVV +GG DE++ P V L DG + Sbjct: 187 ARPTHMLLGVARESLMPLMAETLRRTGAARAAVVFGAGGYDELTPLGPARVLFLRDGIVS 246 Query: 442 SYQLTAEDFGLTPYHQEQLAGGTPEENRDILTRLLQGKGDAAHEAAVAANVAMLMRLHGH 501 +++ +G+ P E L EE +L LL G G A + NV M + L H Sbjct: 247 EHEVDPARYGIAPCTPEDLVVRDREEAVRVLRELLSGAGPQAMRDMLVFNVGMALHLL-H 305 Query: 502 ED 503 +D Sbjct: 306 DD 307 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: 443 Number of extensions: 22 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: 531 Length of database: 332 Length adjustment: 32 Effective length of query: 499 Effective length of database: 300 Effective search space: 149700 Effective search space used: 149700 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: 50 (23.9 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