Align TRAP dicarboxylate transport system, periplasmic component (DctP-like) (characterized, see rationale)
to candidate WP_086511777.1 BZY95_RS20685 C4-dicarboxylate ABC transporter substrate-binding protein
Query= uniprot:G8AR24 (337 letters) >NCBI__GCF_002151265.1:WP_086511777.1 Length = 332 Score = 218 bits (554), Expect = 2e-61 Identities = 119/318 (37%), Positives = 185/318 (58%), Gaps = 7/318 (2%) Query: 12 GLAAAILAPVAASAQDIKPRLIRFGYGLSESSNQGRAVKFFVEDMAKRSGGKLKVKGFAD 71 G+ AA L A +AQ++ G+ LS +S+ + F E + S G V +A Sbjct: 16 GITAAALVANAQAAQEVS-----LGHTLSSTSHYAVGARAFKETLEALSDGAFTVTEYAS 70 Query: 72 ASLGSDIQMQNALIGGAQEMMVGSTATLVGIVKDFAVFDLPFLFNNEQEADAVFDGPFGQ 131 +LG + +M L G ++++ ST L V + V DLPFLF + +A V D G Sbjct: 71 GALGGEREMIEGLQIGTVDVVITSTGPLGNFVPETYVLDLPFLFESYDQARCVLDSELGD 130 Query: 132 KLAAKLNDKGLVGLVYWENGFRNLTNSKRPVEKVEDLKGIKLRVMQNPVYIDMFNGFGAN 191 +L K+ LVGL + ENGFR+LTNS+R V D +G+++R M+N V+ + F GA Sbjct: 131 ELLEKMGQHDLVGLAWSENGFRHLTNSRREVTSPSDAEGLRVRTMENEVHQEAFRQLGAR 190 Query: 192 AVPLSFSELFTAMETGTVDGQENPVTTIQSSKFYEVQKYLTISKHVYSPWIVLASKRWYD 251 P++F ELFTA++ G VDGQENP+T I ++ F+EVQ +L+++ HVYSP VL S D Sbjct: 191 PTPMAFPELFTALQQGVVDGQENPITVIVATNFWEVQDHLSLTGHVYSPAAVLGSPLLLD 250 Query: 252 GLSADERKIINEAAVASRDFERKDSREASKQSIAYLKDKGMQINELSDAELGRMREMVKP 311 GLS +ER+ +EAA AS + R + ++ +A L+D GM +N ++ ++G ++ V+P Sbjct: 251 GLSDEEREWFHEAARASAEATRGEVSRLEEEGVALLRDNGMTVN--TEIDIGPFQQAVEP 308 Query: 312 AMDKFAADGGADLLNELQ 329 A + F G+++L +Q Sbjct: 309 AYEIFTRQHGSEMLERIQ 326 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: 214 Number of extensions: 9 Number of successful extensions: 1 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: 332 Length adjustment: 28 Effective length of query: 309 Effective length of database: 304 Effective search space: 93936 Effective search space used: 93936 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