Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Dsui_2532 Dsui_2532 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__PS:Dsui_2532 Length = 341 Score = 162 bits (409), Expect = 1e-44 Identities = 105/339 (30%), Positives = 184/339 (54%), Gaps = 10/339 (2%) Query: 4 LRSVLLATGLAAAIL--APVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSG 61 ++ ++ A LA A+L A A D K R L + G+A + + E + +++ Sbjct: 1 MKKLVAAASLALALLPLGHSVAHAADYKSEY-RLSTVLGPAFPWGKAGERWAELVKQKTE 59 Query: 62 GKLKVKGFADASL--GSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQ 119 G++ +K + SL G + +A+ G ++ +GS+ VK +F LPFL +E+ Sbjct: 60 GRINIKLYPGTSLVGGDQTREFSAIRQGVIDLAIGSSINWSPQVKQLNLFSLPFLTPDEK 119 Query: 120 EADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNP 179 DA+ GP G+ L A L +G+V L Y ENGFR L+NS+ P+ DLKG+K+RV+ +P Sbjct: 120 SLDALIKGPVGKDLFAVLEKQGVVPLAYGENGFRELSNSRHPIRTPADLKGMKIRVVGSP 179 Query: 180 VYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEV-QKYLTISKHVY 238 ++ID F+ GAN +S+++ A+ T VDGQENP++ ++K + + Q++LT+ ++ Sbjct: 180 IFIDAFSALGANPTQMSWADAQPALATKAVDGQENPLSVFNAAKLHTLGQQHLTLWGYMT 239 Query: 239 SPWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSRE-ASKQSIAYLKD---KGMQI 294 P I + ++ ++ S +RK + EAA + +R+ S A LKD G+ I Sbjct: 240 DPLIFVVNRNVWNNWSEADRKAVREAAEQAAAENLVAARKGVSPGDDALLKDIEKNGVTI 299 Query: 295 NELSDAELGRMREMVKPAMDKFAADGGADLLNELQGEIS 333 L+ + +++ +P DK+A G DL+ + + I+ Sbjct: 300 TRLTAEQRKAFKDLTRPVYDKWAETVGKDLVKKAEAAIA 338 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: 254 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: 337 Length of database: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 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