Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Ac3H11_2073 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2073 Length = 328 Score = 218 bits (554), Expect = 2e-61 Identities = 116/300 (38%), Positives = 179/300 (59%), Gaps = 5/300 (1%) Query: 5 RSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKL 64 R++L A LA A+ P A AQ +K + G+G + + + A F E + ++ G++ Sbjct: 8 RTLLAAAALAVAL--PGLAQAQAMK---LTLGHGAAPGNPRHEAAVKFAETLKAKTAGRI 62 Query: 65 KVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAV 124 +V+ A LG D M A+ GA +M S + V ++A + +PF+F+ +A + Sbjct: 63 EVQVAPSAQLGDDAAMVTAVRTGALDMTANSQGAVSVAVPEYAAYGMPFMFSTPAQAFKL 122 Query: 125 FDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDM 184 DGP GQ+LA K DKG+V L YW+NG R++TNSKRP+ KVED+KG+K+R + V +D+ Sbjct: 123 LDGPLGQELAQKSADKGMVVLGYWDNGIRHMTNSKRPITKVEDMKGLKMRTPPDAVLVDI 182 Query: 185 FNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVL 244 GA A + F+EL+ A++ G VDGQENP+ I +SK YEVQK+L ++ H++ L Sbjct: 183 MQALGAEAQQIKFAELYVALQQGVVDGQENPLVNIHASKLYEVQKHLALTSHMFQMTPFL 242 Query: 245 ASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGR 304 SKR +D LS +RK + EAA + +RK S+EA + + LK KG+Q+ + A + Sbjct: 243 MSKRTWDRLSDADRKAVTEAAAEATALQRKMSQEADDKLLDDLKAKGVQVTTVDKAAFAK 302 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: 239 Number of extensions: 7 Number of successful extensions: 1 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: 328 Length adjustment: 28 Effective length of query: 309 Effective length of database: 300 Effective search space: 92700 Effective search space used: 92700 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