Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate WP_068003513.1 PsAD2_RS05435 DctP family TRAP transporter solute-binding subunit
Query= uniprot:I7END8 (333 letters) >NCBI__GCF_001623255.1:WP_068003513.1 Length = 333 Score = 391 bits (1005), Expect = e-113 Identities = 193/330 (58%), Positives = 246/330 (74%), Gaps = 1/330 (0%) Query: 2 KFVTAAATAVALTMSAGTAMA-ACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMN 60 K +TAA A + + T A ACD GE+V+KFSHV + HPKG A+ L +R+N EMN Sbjct: 3 KIITAATVAAGMFTATQTVAAEACDPGEVVIKFSHVVSATGHPKGDFATALAERVNTEMN 62 Query: 61 GTMCLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAV 120 G C++V+P+S L++D+KV+EA+L GDVQ+AAPSLSKFE +T ++R+FDLPF+F +++AV Sbjct: 63 GKACMQVFPSSQLFDDDKVMEALLLGDVQIAAPSLSKFEAYTLKYRVFDLPFLFSDMNAV 122 Query: 121 DAFQGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSANKPLINPSDANGLKFRVQSSDVLV 180 + F GQ +L +M G GL Y +NG+K SANKPL+ P+DA GLKFRVQ+SDV V Sbjct: 123 NNFTQGPTGQELLGAMSDIGFVGLGYVYNGIKHFSANKPLLTPADAAGLKFRVQTSDVAV 182 Query: 181 AQMEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYL 240 A +EA+ + QK+AF EVYGALQ GVVDGQENTWSNIY KKFFEVQDG+TET+H L YL Sbjct: 183 AMIEAMEANAQKLAFKEVYGALQTGVVDGQENTWSNIYTKKFFEVQDGITETSHQLLSYL 242 Query: 241 VVTSVDWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQR 300 VTS +WLDSLDP VR+QF+TI EVT N+ S+ +N +Q II++G VR LTPEQR Sbjct: 243 AVTSQEWLDSLDPEVRDQFVTIFTEVTNEANARSSAINEANKQKIIESGVEVRTLTPEQR 302 Query: 301 AAWVEAMKPVWEQFAGDVGQDMIDAAQAIN 330 WV MKPVW +FA D+GQD+IDAA A N Sbjct: 303 EQWVVVMKPVWAKFADDIGQDVIDAAVAAN 332 Lambda K H 0.316 0.130 0.371 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: 339 Number of extensions: 6 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: 333 Length of database: 333 Length adjustment: 28 Effective length of query: 305 Effective length of database: 305 Effective search space: 93025 Effective search space used: 93025 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 (21.6 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