Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_011383337.1 AMB_RS04560 C4-dicarboxylate ABC transporter
Query= SwissProt::P37735 (333 letters) >NCBI__GCF_000009985.1:WP_011383337.1 Length = 337 Score = 441 bits (1134), Expect = e-128 Identities = 221/321 (68%), Positives = 260/321 (80%), Gaps = 3/321 (0%) Query: 7 LGALVGATALSLALSVPALAE---PIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVD 63 LG L+ + L+ A+A+ PIVIKFSHVVAPDTPKGKGA F++LAE+ T G V Sbjct: 3 LGTLIAGAIAACVLAGSAMAQQAQPIVIKFSHVVAPDTPKGKGAEYFKKLAEERTKGRVK 62 Query: 64 VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKV 123 VEVYPNSQLYKDKEE+EALQLGAVQMLAPSLAKFGPLGV++FEVFDLPYIF + L V Sbjct: 63 VEVYPNSQLYKDKEEMEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKDVLRSV 122 Query: 124 TQGEAGKMLLSKLEAKGITGLAFWDNGFKIMSANTPLTMPDDFLGLKMRIQSSKVLEAEM 183 T G G LL KLE KGI GLA+WDNGFKIMSAN P+ P D G+KMRIQSSKVL+AEM Sbjct: 123 TGGPVGASLLKKLEGKGIIGLAYWDNGFKIMSANKPIKAPSDLKGVKMRIQSSKVLDAEM 182 Query: 184 NALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIV 243 ALGA+PQVMAFSEVYQALQTGVVDGTENPPSNM+TQKM+EVQKHAT++NHGYLGYAVIV Sbjct: 183 RALGALPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQKHATMTNHGYLGYAVIV 242 Query: 244 NKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGTTEFHELTAEERAA 303 NK+FW+GLPAD+R LE AM+E++ +AN IA+ EN+ A++AMK +G TEFH+ +A E A Sbjct: 243 NKKFWEGLPADIRATLEGAMSEASVFANAIAQTENDDAVKAMKASGKTEFHDPSAAEIEA 302 Query: 304 WEEVLTPVHDEMAERIGAETI 324 W + L PVH +M R+G + I Sbjct: 303 WRKALLPVHKDMEGRVGKDLI 323 Lambda K H 0.314 0.130 0.364 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: 364 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: 333 Length of database: 337 Length adjustment: 28 Effective length of query: 305 Effective length of database: 309 Effective search space: 94245 Effective search space used: 94245 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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