Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_090447096.1 BLS63_RS17680 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_900100495.1:WP_090447096.1 Length = 335 Score = 161 bits (408), Expect = 2e-44 Identities = 97/328 (29%), Positives = 178/328 (54%), Gaps = 7/328 (2%) Query: 5 RSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKL 64 ++++ A L+ L A S+Q P +I+F + +++++ +G+ F + +R G++ Sbjct: 7 KALVCALSLSLGSLVQAAGSSQTA-PIVIKFAHVVADNTPKGQGALLFKQLAEERLPGRV 65 Query: 65 KVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAV 124 +V+ + ++SL D + AL+ G +++ S A K +FDLPFLF++ A+ Sbjct: 66 RVEVYPNSSLFGDGKEMEALLLGDVQLLAPSLAKFEQYAKPIQIFDLPFLFDDLAAAERF 125 Query: 125 FDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDM 184 P G+ L + DK + GL YW NG + ++ +K P+ + +D +G+K RV + V + Sbjct: 126 QSSPQGKALLTSMEDKNITGLAYWHNGTKQMSANK-PLREPKDARGLKFRVQASAVLEEQ 184 Query: 185 FNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVL 244 F AN +SF+E++ ++TG V+G EN + QS K +EVQKY+T S H ++++ Sbjct: 185 FKAVRANPRKMSFAEVYQGLQTGVVNGTENTWSNYQSQKVHEVQKYMTESNHGLIDYMLI 244 Query: 245 ASKRWYDGLSAD---ERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAE 301 + ++ GL AD E + I + + + +++KQ+IA +I EL+ + Sbjct: 245 TNTTFWKGLPADVRSELQAIMAEVTVEVNKQADELNQSAKQAIAAAGT--TEIIELTAEQ 302 Query: 302 LGRMREMVKPAMDKFAADGGADLLNELQ 329 + RE +KP KF A+ GA+L+ Q Sbjct: 303 RAQWREAMKPVWQKFEAEIGAELIEAAQ 330 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: 196 Number of extensions: 12 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: 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 24 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