Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate GFF2082 Psest_2125 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__psRCH2:GFF2082 Length = 338 Score = 137 bits (345), Expect = 4e-37 Identities = 86/282 (30%), Positives = 151/282 (53%), Gaps = 10/282 (3%) Query: 42 AEQNMGKKLEDASNGEITFKMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVN 101 A + + +++ AS G++ + FA LGS+ ++ GA +M S + + ++ Sbjct: 49 AAKLLAEEVAKASGGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMA 108 Query: 102 VFNMPFVFRDHDHMRKIIDGEIGQEILDKITNSDFNLVALAWMDGGSRSIYTK-KPVRSL 160 V++ PF+F D +++DG +G++++DK+ LV L + + G R++ +P+ L Sbjct: 109 VWDTPFLFTDPRQADQVLDGPVGRQVMDKLEEK--GLVGLVYWENGFRNVTNSARPIEKL 166 Query: 161 EDLKGMKIRVQGNPLFIDMMNAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHF 220 ED G+K+RV NP+FID MG N + + E+F+AL+T +DG EN T+L + Sbjct: 167 EDFNGVKLRVMPNPVFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFY 226 Query: 221 QSAKYYTLTGHLILPEPVVMSKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEE 280 + KY ++T H+ P V +SK W+ LS +Q ++ + A +A+ ER +++ + Sbjct: 227 EVQKYLSVTNHVYSPWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALA 286 Query: 281 KLKAAGVEFITVDKKPFYDATASVREKYGAQYADLMKRIDAV 322 LK G++ V D +REK AQ A + IDAV Sbjct: 287 ALKERGMQINEVSP----DEIQRMREK--AQPA-IQTVIDAV 321 Lambda K H 0.318 0.134 0.381 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: 229 Number of extensions: 10 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: 323 Length of database: 338 Length adjustment: 28 Effective length of query: 295 Effective length of database: 310 Effective search space: 91450 Effective search space used: 91450 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 (21.7 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