Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate Echvi_3629 Echvi_3629 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__Cola:Echvi_3629 Length = 335 Score = 151 bits (382), Expect = 2e-41 Identities = 84/264 (31%), Positives = 148/264 (56%) Query: 31 RLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKGFADASLGSDIQMQNALIGGAQE 90 R+I+ G+GL A+ + + + ++S GKL +K + +A LG++ ++ L G+ Sbjct: 35 RVIKLGHGLDTKHPVHEAMLYMAKRLEEKSDGKLTMKVYPNAQLGNERELVELLQIGSLG 94 Query: 91 MMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGPFGQKLAAKLNDKGLVGLVYWEN 150 M S+A + V P+LF + + V +G G++L + L GL +++ Sbjct: 95 MTKVSSAVMESFAPKIQVLSQPYLFRDNGHRERVLNGEIGKRLLNEGTQFWLKGLCFYDA 154 Query: 151 GFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGFGANAVPLSFSELFTAMETGTVD 210 G R+ +PVE EDL G K+RVM++ I+M N FG + P+S+ EL+TA++ G VD Sbjct: 155 GSRSFYTKDKPVESPEDLVGKKIRVMESNTAINMVNSFGGSPTPVSWGELYTALQQGIVD 214 Query: 211 GQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKRWYDGLSADERKIINEAAVASRD 270 G EN ++ SS+ YE+ K+ ++ +H P +++ S + +D LS +E+ + EAA S Sbjct: 215 GAENNPPSVISSRHYEICKFYSLDEHTAVPDMLIVSTKVWDRLSEEEQNWLQEAADESAK 274 Query: 271 FERKDSREASKQSIAYLKDKGMQI 294 F+ K EA ++S+ L+ +G+ I Sbjct: 275 FQYKIWAEAEEESMRQLEAEGVTI 298 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: 246 Number of extensions: 15 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: 335 Length adjustment: 28 Effective length of query: 309 Effective length of database: 307 Effective search space: 94863 Effective search space used: 94863 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