Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_011383337.1 AMB_RS04560 C4-dicarboxylate ABC transporter
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_000009985.1:WP_011383337.1 Length = 337 Score = 182 bits (462), Expect = 1e-50 Identities = 106/336 (31%), Positives = 190/336 (56%), Gaps = 6/336 (1%) Query: 1 MKLLRSVLLATGLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRS 60 MKL L+A +AA +LA +A AQ +P +I+F + ++ + +G+ ++F + +R+ Sbjct: 1 MKL--GTLIAGAIAACVLAG-SAMAQQAQPIVIKFSHVVAPDTPKGKGAEYFKKLAEERT 57 Query: 61 GGKLKVKGFADASLGSDIQMQNALIGGAQEMMVGSTATLVGI-VKDFAVFDLPFLFNNEQ 119 G++KV+ + ++ L D + AL GA +M+ S A + VK+F VFDLP++F ++ Sbjct: 58 KGRVKVEVYPNSQLYKDKEEMEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKD 117 Query: 120 EADAVFDGPFGQKLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNP 179 +V GP G L KL KG++GL YW+NGF+ + ++ +P++ DLKG+K+R+ + Sbjct: 118 VLRSVTGGPVGASLLKKLEGKGIIGLAYWDNGFK-IMSANKPIKAPSDLKGVKMRIQSSK 176 Query: 180 VYIDMFNGFGANAVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYS 239 V GA ++FSE++ A++TG VDG ENP + + + K +EVQK+ T++ H Y Sbjct: 177 VLDAEMRALGALPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQKHATMTNHGYL 236 Query: 240 PWIVLASKRWYDGLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKG-MQINELS 298 + V+ +K++++GL AD R + A + F ++ + ++ +K G + ++ S Sbjct: 237 GYAVIVNKKFWEGLPADIRATLEGAMSEASVFANAIAQTENDDAVKAMKASGKTEFHDPS 296 Query: 299 DAELGRMREMVKPAMDKFAADGGADLLNELQGEISK 334 AE+ R+ + P G DL+ E +K Sbjct: 297 AAEIEAWRKALLPVHKDMEGRVGKDLIESFYKEAAK 332 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: 252 Number of extensions: 11 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: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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