Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate H281DRAFT_03359 H281DRAFT_03359 tripartite ATP-independent transporter solute receptor, DctP family
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__Burk376:H281DRAFT_03359 Length = 342 Score = 144 bits (363), Expect = 3e-39 Identities = 89/298 (29%), Positives = 155/298 (52%), Gaps = 7/298 (2%) Query: 5 RSVLLATGLAAAI-----LAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKR 59 R+ L G AA L P A AQ + +L ++ L+ S K + + K Sbjct: 7 RTFLQTLGAAAVATTGTGLFPSLACAQTAQFKL-KYANNLALSHPLNVRAKEAADAIRKE 65 Query: 60 SGGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQ 119 +GG++ ++ F + +G+D M + + GA + + L +V A+ + F F + Sbjct: 66 TGGRVDLQIFPNGQMGTDTDMLSQVRSGAIDFLTQGGVVLSTLVPVSAINGIGFAFKDYN 125 Query: 120 EADAVFDGPFGQKLAAKLNDKGLVGLVY-WENGFRNLTNSKRPVEKVEDLKGIKLRVMQN 178 + A DG G + ++ GL+ + W+NGFR+LT+S +PV DLKG+K+RV + Sbjct: 126 QVWAAMDGDLGSYIRRAVSKVGLIAMEKPWDNGFRHLTSSVKPVLSPTDLKGLKIRVPVS 185 Query: 179 PVYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVY 238 P++ MF A+ ++FSE ++A++T VD +ENP+ I++ +FYEVQKY +++ H++ Sbjct: 186 PLWTSMFKALDASPTSINFSEAYSALQTKVVDAEENPLALIETGRFYEVQKYCSLTGHIW 245 Query: 239 SPWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINE 296 + LA+ R + L D + I+ + A+ ER D S + L+ GM N+ Sbjct: 246 DGFWFLANARSWGNLPPDLQTIVAKHLNAAAVAERADVAALSTSLVETLRSHGMAFNK 303 Lambda K H 0.317 0.134 0.372 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: 242 Number of extensions: 9 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: 337 Length of database: 342 Length adjustment: 28 Effective length of query: 309 Effective length of database: 314 Effective search space: 97026 Effective search space used: 97026 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 Sep 17 2021. The underlying query database was built on Sep 17 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