Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_002721134.1 RSPH17029_RS12960 TRAP transporter substrate-binding protein
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_000015985.1:WP_002721134.1 Length = 334 Score = 177 bits (450), Expect = 3e-49 Identities = 103/319 (32%), Positives = 179/319 (56%), Gaps = 6/319 (1%) Query: 9 LATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKG 68 LA A A+ A V A AQ P +I+F + ++ + +G+ F E K + G + V+ Sbjct: 10 LAGAAALALAAAVPALAQ---PIVIKFSHVVAPDTPKGKGATKFEELAEKYTDGAVDVEV 66 Query: 69 FADASLGSDIQMQNALIGGAQEMMVGSTATLVGI-VKDFAVFDLPFLFNNEQEADAVFDG 127 + ++ L D + AL GA +M+ S A + V+DF VFDLP++F V +G Sbjct: 67 YPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKGYDALHTVTNG 126 Query: 128 PFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNG 187 G+ L +KL DKG+ GL YW+NGF+ + ++ P+ +D G+K+R+ + V N Sbjct: 127 EVGKMLFSKLEDKGIKGLAYWDNGFK-IMSANSPIATPDDFLGLKMRIQSSKVLEAQMNA 185 Query: 188 FGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASK 247 GA ++FSE++ A++TG VDG ENP + + + K +EVQK+ T+S H Y + V+ +K Sbjct: 186 LGAVPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQKHATVSNHGYLGYAVIVNK 245 Query: 248 RWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKG-MQINELSDAELGRMR 306 +++DGL + R + +A + D+ ++E + +++ +KD G + +EL+ EL Sbjct: 246 QFWDGLPEEVRAGLEKALTEATDYANGIAKEENDKALQAMKDAGTTEFHELTPEELAAWE 305 Query: 307 EMVKPAMDKFAADGGADLL 325 E++ P ++ A GA+ + Sbjct: 306 EVLAPVHEEMAGRIGAETI 324 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: 250 Number of extensions: 13 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: 334 Length adjustment: 28 Effective length of query: 309 Effective length of database: 306 Effective search space: 94554 Effective search space used: 94554 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 Apr 10 2024. 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