Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_004318960.1 C665_RS14785 TRAP transporter substrate-binding protein DctP
Query= SwissProt::P37735 (333 letters) >NCBI__GCF_000310185.1:WP_004318960.1 Length = 346 Score = 182 bits (463), Expect = 8e-51 Identities = 116/341 (34%), Positives = 176/341 (51%), Gaps = 15/341 (4%) Query: 2 LTRRILGALVGATALSLA----------LSVPALAEPIVIKFSHVVAPDTPKGKGAAKFE 51 L RRIL + A +LA + A + +VIK H KG +F Sbjct: 9 LRRRILATGLALAAFALAGCSGEQKGTQPATTATNQKLVIKVGHAATESNTGHKGLVEFN 68 Query: 52 ELAEKYTNGAVDVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLP 111 L + T G + +E+YPNSQL ++E +EA+QLG+V M S A G ++F DLP Sbjct: 69 RLLGEKTGGRISLEIYPNSQLGSERELIEAVQLGSVGMTFVSSAPLGGFK-KEFFALDLP 127 Query: 112 YIFKDYEALHKVTQGEAGKMLLSKLEAKGITGLAFWDNGFKIMS-ANTPLTMPDDFLGLK 170 ++FKD ++KV GE G+ LL L+ I GL FW+NGF+ +S + + PDD G+K Sbjct: 128 FVFKDRPTVYKVLDGEPGQYLLKSLQDINIQGLGFWENGFRQLSNSKVAVKTPDDLKGIK 187 Query: 171 MRIQSSKVLEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHAT 230 MR ++V A LGA P +AF E++ ALQ G D E P + K EVQK T Sbjct: 188 MRTMENEVHLAAWKELGANPAPLAFGELFTALQQGTFDAQETPINLFRDMKFFEVQKFIT 247 Query: 231 VSNHGYLGYAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQAMKDAGT 290 + H Y + ++++K +DGL + + +A + Y +A++ + +A M G Sbjct: 248 KTGHLYSPFVILMSKPLYDGLSEADKQAMAEAFEAAKAYQRDLAQKSDAEAEAQM--TGI 305 Query: 291 TEFHELTAEERAAWEEVLTPVHDEMAERIGAETIAAVKAAT 331 T F EL+ E+ A+ + PV+D + ++ G E + V AT Sbjct: 306 T-FTELSDAEKEAFRAKMGPVYDLVKKKAGEEIVKKVLQAT 345 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: 263 Number of extensions: 10 Number of successful extensions: 3 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: 346 Length adjustment: 28 Effective length of query: 305 Effective length of database: 318 Effective search space: 96990 Effective search space used: 96990 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 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