Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_010628110.1 BZY95_RS12945 TRAP transporter substrate-binding protein
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_002151265.1:WP_010628110.1 Length = 356 Score = 222 bits (566), Expect = 1e-62 Identities = 124/344 (36%), Positives = 198/344 (57%), Gaps = 19/344 (5%) Query: 5 RSVLLATGLAAAILAPVAASAQDIKP--------------RLIRFGYGLSESSNQGRAVK 50 R+ L G A L A A D+ +R G GLS++S Q + + Sbjct: 6 RNTLTLAGAATLSLGIAYAQAPDLSDPPAIEGEAVGDHGSHTLRMGLGLSDTSPQYLSSR 65 Query: 51 FFVEDMAKRSGGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFD 110 +F + + +R+ G++ V F ++ LG D+QM L G+ +M S++ V++ AVFD Sbjct: 66 YFADILEQRTEGRITVNIFPNSQLGDDVQMMEMLQTGSLDMSYPSSSPATTYVQELAVFD 125 Query: 111 LPFLFNNEQEADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDL-- 168 LPFL + + A AV Q++ G+ L + ENG+R LTNS R VE ED+ Sbjct: 126 LPFLLPSREAAIAVMQSDTAQRMLDAFEGTGIKALTFSENGYRQLTNSARAVESPEDVAG 185 Query: 169 ---KGIKLRVMQNPVYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFY 225 +G+ +R M+NPV++ ++ GAN P++F ELF+AME G VDGQENP +TI +S FY Sbjct: 186 LDVRGLSVRTMENPVHLSIWETLGANPTPMAFGELFSAMEQGVVDGQENPWSTILTSNFY 245 Query: 226 EVQKYLTISKHVYSPWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIA 285 EVQ Y + ++HVY+P+I++ S+R +D L+ + ++++ EAA S ++E + S E + Sbjct: 246 EVQDYGSETRHVYTPFIMMMSQRTWDRLAPEYQELVQEAARLSAEYEIQLSTEYDDWARD 305 Query: 286 YLKDKGMQINELSDAELGRMREMVKPAMDKFAADGGADLLNELQ 329 L+++GMQI L D ++ +E V+P D++A G DL+ E+Q Sbjct: 306 QLEERGMQITRLDDDQVAAFQEAVQPVYDRWAPRIGEDLIAEIQ 349 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: 234 Number of extensions: 6 Number of successful extensions: 2 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: 356 Length adjustment: 29 Effective length of query: 308 Effective length of database: 327 Effective search space: 100716 Effective search space used: 100716 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