Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_011842336.1 RSPH17029_RS17115 DctP family TRAP transporter solute-binding subunit
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_000015985.1:WP_011842336.1 Length = 331 Score = 245 bits (625), Expect = 1e-69 Identities = 122/309 (39%), Positives = 192/309 (62%) Query: 9 LATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKG 68 L GL AA L A AQD R I+F E + + + F + + ++SGGKLK + Sbjct: 3 LIHGLLAAALLATGAQAQDYSSRTIKFAATGQEGTPPVQGMHIFAQKLEEQSGGKLKTRV 62 Query: 69 FADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGP 128 FA+ LG D+Q+ ++L GG EMMV + ++ +DF + DLPF++ +E+ D + DG Sbjct: 63 FANGVLGGDVQVLSSLQGGVVEMMVWNAGNMMTQAQDFGILDLPFIYQDEEVMDTLLDGE 122 Query: 129 FGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGF 188 G+KL +L + G++GL +WE GFR LTN R V ++ED+ G+K+RV QNP+ +DM+ Sbjct: 123 VGRKLTDQLPEHGVIGLSFWEQGFRQLTNDTREVHRLEDIAGLKVRVQQNPLLVDMWKAL 182 Query: 189 GANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKR 248 GAN P++ +EL+TA+ETG VDGQE ++K+ EVQKYL++++H Y+P IVL K Sbjct: 183 GANPTPMAVTELYTALETGAVDGQECTAPFALTAKYTEVQKYLSVTRHNYNPQIVLIGKP 242 Query: 249 WYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGRMREM 308 ++D L+ DE+ +I + A + +R+ SR A ++ ++ G + E++ EL RM+E Sbjct: 243 FWDKLTDDEKALIQKVAQETAVEQRRISRAAQDSALEEIRAAGNVVTEITPEELARMQEA 302 Query: 309 VKPAMDKFA 317 V P + +A Sbjct: 303 VAPVIRTYA 311 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: 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: 331 Length adjustment: 28 Effective length of query: 309 Effective length of database: 303 Effective search space: 93627 Effective search space used: 93627 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 Apr 10 2024. 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