Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate GFF2914 PS417_14910 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__WCS417:GFF2914 Length = 327 Score = 160 bits (404), Expect = 5e-44 Identities = 103/328 (31%), Positives = 176/328 (53%), Gaps = 13/328 (3%) Query: 1 MKLLRSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRS 60 +KL R++L A L AA LA A P +I+F + ++E++ +G+ F + +R Sbjct: 2 LKLSRALLCAATLFAAGLAQAA------DPIVIKFAHVVAENTPKGQGALLFKKLAQERL 55 Query: 61 GGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQE 120 G++KV+ + ++SL D + AL+ G +M+ S A + ++DLPFLFN+ Sbjct: 56 PGRVKVEVYPNSSLFGDGKEMEALLLGDVQMLAPSLAKFEQYTQQVQIYDLPFLFNDLAA 115 Query: 121 ADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPV 180 D F G+ L + DK ++GL YW NG + L+++K + + +D +G+K RV + V Sbjct: 116 VDR-FQAAQGKALLTAMQDKNILGLAYWHNGLKQLSSNKA-LHEPKDARGLKFRVQASSV 173 Query: 181 YIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSP 240 + F AN +SF+E++ ++TGTV+G EN + +S K EVQKY T S H Sbjct: 174 LEEQFKAIRANPRKMSFAEVYQGLQTGTVNGTENTWSNYESQKVNEVQKYFTESNHGLID 233 Query: 241 WIVLASKRWYDGLSADERKIINEAAVASRDFERKDS---REASKQSIAYLKDKGMQINEL 297 ++V+ + +++GL D R + + V K + +++KQ I + K +I EL Sbjct: 234 YMVITNATFWNGLPPDIRSTLEQIMVEVTVEVNKQAEALNQSAKQKI--IDAKTSEIIEL 291 Query: 298 SDAELGRMREMVKPAMDKFAADGGADLL 325 + + RE ++P KF + GADL+ Sbjct: 292 TPEQRQLWREAMRPVWQKFEGEIGADLI 319 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: 209 Number of extensions: 9 Number of successful extensions: 4 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: 327 Length adjustment: 28 Effective length of query: 309 Effective length of database: 299 Effective search space: 92391 Effective search space used: 92391 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