Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate RR42_RS06535 RR42_RS06535 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >FitnessBrowser__Cup4G11:RR42_RS06535 Length = 342 Score = 182 bits (463), Expect = 8e-51 Identities = 113/333 (33%), Positives = 186/333 (55%), Gaps = 8/333 (2%) Query: 9 LATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKG 68 LA +AAA LAP A AQ K + L + G+ + + + + +R+ G++ +K Sbjct: 10 LAATIAAAALAPAGAMAQSYKAEY-KMSLVLGPAFPWGKGGEIWADLVRQRTSGRINIKL 68 Query: 69 FADASL--GSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFD 126 + SL G + +A+ G +M VGST VK+ +F LPFL + + DA+ Sbjct: 69 YPGTSLVAGDQTREFSAIRQGVIDMAVGSTINWSPQVKELNLFSLPFLMPDYKALDALTQ 128 Query: 127 GPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFN 186 G G+ + A L+ G+V L + ENGFR ++NSKR + K EDLKG+KLRV+ +P+YI+ FN Sbjct: 129 GEVGKSIFATLDKSGVVPLAWGENGFREVSNSKREIRKPEDLKGMKLRVVGSPLYIETFN 188 Query: 187 GFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEV-QKYLTISKHVYSPWIVLA 245 GAN +S+++ AM +G VDGQENP + ++K Y V QKY+T +V P I + Sbjct: 189 ALGANPTQMSWADAQPAMASGAVDGQENPQSVFAAAKLYTVGQKYVTTWGYVADPLIFVV 248 Query: 246 SKRWYDGLSADERKIINEAAVASRDFE----RKDSREASKQSIAYLKDKGMQINELSDAE 301 +K+ ++ + +R+I+ +AA+ + E RK EA + ++ G+++ +L+ AE Sbjct: 249 NKQIWESWTPADREIVKQAAIDAGKQETALARKGLVEAGAPAWKDMEAHGVKVAQLTPAE 308 Query: 302 LGRMREMVKPAMDKFAADGGADLLNELQGEISK 334 R+ DK+ G DL+++ + I+K Sbjct: 309 HDAFRKATAKVYDKWKKQIGVDLVSKAEASIAK 341 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: 231 Number of extensions: 10 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: 342 Length adjustment: 28 Effective length of query: 309 Effective length of database: 314 Effective search space: 97026 Effective search space used: 97026 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