Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate WP_068003520.1 PsAD2_RS05450 DctP family TRAP transporter solute-binding subunit
Query= uniprot:I7END8 (333 letters) >NCBI__GCF_001623255.1:WP_068003520.1 Length = 337 Score = 365 bits (937), Expect = e-106 Identities = 181/327 (55%), Positives = 232/327 (70%), Gaps = 1/327 (0%) Query: 5 TAAATAVALTMSAGT-AMAACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMNGTM 63 TA A+ + A A C GE+V+KFSHV HPKG A +L +R+N E+NG Sbjct: 6 TAVILALGIVFGAPAFAQIDCKPGEVVIKFSHVVPPSGHPKGDFARMLAERVNTELNGKA 65 Query: 64 CLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAF 123 C++V+P S LY+D KV+EA++ GDVQLAAPSLSK E +T ++RLFDLPF+F+++DAV F Sbjct: 66 CMQVFPFSQLYDDEKVMEALILGDVQLAAPSLSKLEVYTNKYRLFDLPFLFEDMDAVQRF 125 Query: 124 QGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSANKPLINPSDANGLKFRVQSSDVLVAQM 183 SE GQ +L M G+ GL Y +G+K SA+KPL+ PSD GLKFRVQ+SDV VA + Sbjct: 126 TASEKGQELLGVMSDFGVVGLGYLFDGLKHFSADKPLLVPSDGAGLKFRVQNSDVAVAMI 185 Query: 184 EAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYLVVT 243 EA+G S QK+AF EVYGALQ GVVDGQEN+WSNI+ +FFEVQDG TETNH L Y+V T Sbjct: 186 EAMGASAQKLAFKEVYGALQLGVVDGQENSWSNIFTSRFFEVQDGTTETNHQLLAYVVFT 245 Query: 244 SVDWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQRAAW 303 +WL+SL+P VRE FLTI E N ++ K + RQ I+DAG VRELTP+QR W Sbjct: 246 PQEWLESLEPDVRELFLTIFRETLVKANGQAAKTSEVNRQRIVDAGYTVRELTPKQRQQW 305 Query: 304 VEAMKPVWEQFAGDVGQDMIDAAQAIN 330 V+ M+PVW F ++G+D+IDAA+A N Sbjct: 306 VDVMRPVWGDFEDEIGKDLIDAAEAAN 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: 315 Number of extensions: 10 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 ( 7.3 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