Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate Ac3H11_2073 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:I7END8 (333 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2073 Length = 328 Score = 114 bits (285), Expect = 3e-30 Identities = 82/273 (30%), Positives = 132/273 (48%), Gaps = 10/273 (3%) Query: 42 HPKGIAASLLEKRINEEMNGTMCLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKF 101 +P+ AA + + + G + ++V P++ L +D ++ A+ G + + A S Sbjct: 41 NPRHEAAVKFAETLKAKTAGRIEVQVAPSAQLGDDAAMVTAVRTGALDMTANSQGAVSVA 100 Query: 102 TKQFRLFDLPFMFKNIDAVDAFQGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSANK-PL 160 ++ + +PFMF GQ + +G+ L YW NG++ M+ +K P+ Sbjct: 101 VPEYAAYGMPFMFSTPAQAFKLLDGPLGQELAQKSADKGMVVLGYWDNGIRHMTNSKRPI 160 Query: 161 INPSDANGLKFRVQSSDVLVAQMEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGK 220 D GLK R VLV M+A+G Q++ F+E+Y ALQQGVVDGQEN NI+ Sbjct: 161 TKVEDMKGLKMRTPPDAVLVDIMQALGAEAQQIKFAELYVALQQGVVDGQENPLVNIHAS 220 Query: 221 KFFEVQDGVTETNHGALDYLVVTSVDWLDSLDPAVREQFLTILGEVTATRNSESTKVNAE 280 K +EVQ + T+H + S D L A R+ E TA + K++ E Sbjct: 221 KLYEVQKHLALTSHMFQMTPFLMSKRTWDRLSDADRKAVTEAAAEATALQR----KMSQE 276 Query: 281 ARQSIID---AGGVVRELTPEQRAAWVEAMKPV 310 A ++D A GV ++T +AA+ +A V Sbjct: 277 ADDKLLDDLKAKGV--QVTTVDKAAFAKATAAV 307 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: 232 Number of extensions: 14 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: 328 Length adjustment: 28 Effective length of query: 305 Effective length of database: 300 Effective search space: 91500 Effective search space used: 91500 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 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