Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate GFF362 Psest_0363 tripartite ATP-independent periplasmic transporter solute receptor, DctP family
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__psRCH2:GFF362 Length = 323 Score = 508 bits (1308), Expect = e-149 Identities = 252/323 (78%), Positives = 282/323 (87%) Query: 1 MTFKRKLLLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITF 60 M KRKLL+ LPFAF ++ A A+ +K AEIHPAGYPTVVA +N+GKKLE A+NGEI Sbjct: 1 MNLKRKLLVTALPFAFCISGLAHAMTLKIAEIHPAGYPTVVAMENLGKKLETATNGEIKS 60 Query: 61 KMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIID 120 +MFAGGVLGSEKEVIEQ QIGAVQ+TRVSLG VGPVVP NVFNMPFVFRD DHMRK++D Sbjct: 61 RMFAGGVLGSEKEVIEQTQIGAVQLTRVSLGSVGPVVPATNVFNMPFVFRDIDHMRKVVD 120 Query: 121 GEIGQEILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPLFIDMM 180 GEIGQEILD ITNSDFN+V LAWM+ GSRS+YTKKP+R +EDLKGMKIRV GNPLFID + Sbjct: 121 GEIGQEILDAITNSDFNMVGLAWMEAGSRSLYTKKPIRRIEDLKGMKIRVIGNPLFIDTL 180 Query: 181 NAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVM 240 NAMG NGIAMDTGEIFSALQ+GVIDGAENN PTLLEHNHF+ AK+YT T HLILPEP++M Sbjct: 181 NAMGANGIAMDTGEIFSALQSGVIDGAENNSPTLLEHNHFRVAKHYTQTHHLILPEPLLM 240 Query: 241 SKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDKKPFYDA 300 SK TWNKLSPEQQA VKK+A+EAQ+EER LW AK AS EKLKA GVEFI VD KPFYDA Sbjct: 241 SKDTWNKLSPEQQATVKKLAKEAQLEERDLWVAKETASNEKLKAEGVEFIEVDTKPFYDA 300 Query: 301 TASVREKYGAQYADLMKRIDAVQ 323 TA VREKYGAQ+A+L+KRI+AVQ Sbjct: 301 TAPVREKYGAQFAELIKRIEAVQ 323 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: 355 Number of extensions: 14 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: 323 Length of database: 323 Length adjustment: 28 Effective length of query: 295 Effective length of database: 295 Effective search space: 87025 Effective search space used: 87025 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: 48 (23.1 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