Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate Pf6N2E2_487 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_487 Length = 322 Score = 518 bits (1334), Expect = e-152 Identities = 255/323 (78%), Positives = 283/323 (87%), Gaps = 1/323 (0%) Query: 1 MTFKRKLLLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITF 60 M FKR LL+A LP AF +A A ALDIK A+IHP GYPTVVAE++MGK LE SNGE+ F Sbjct: 1 MNFKRTLLIAALPLAF-LAQAAHALDIKIADIHPKGYPTVVAEESMGKTLEKESNGELKF 59 Query: 61 KMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIID 120 K F GGVLGSEKEVIEQ Q GAVQM+RVSLGIVGPVVPDVNVFNMPF+FRD HMR +ID Sbjct: 60 KYFPGGVLGSEKEVIEQMQTGAVQMSRVSLGIVGPVVPDVNVFNMPFIFRDQAHMRAVID 119 Query: 121 GEIGQEILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPLFIDMM 180 G++G ILD+ITNS+F LVALAWMDGG+R++YTKKPV LEDLKGMKIRVQGNP+FI+ Sbjct: 120 GDVGDAILDRITNSEFGLVALAWMDGGTRNLYTKKPVHKLEDLKGMKIRVQGNPMFIETF 179 Query: 181 NAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVM 240 NAMG NGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNH+Q+AKYY+LTGHLILPEP+VM Sbjct: 180 NAMGANGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHYQNAKYYSLTGHLILPEPIVM 239 Query: 241 SKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDKKPFYDA 300 SK TWNKL+PEQQ +VKK A+ AQ EER LWD KS ASEEKLKAAGVEFITVDKKPFYDA Sbjct: 240 SKITWNKLTPEQQDMVKKAAKAAQAEERVLWDKKSTASEEKLKAAGVEFITVDKKPFYDA 299 Query: 301 TASVREKYGAQYADLMKRIDAVQ 323 TA +R KYGA YADL+KRI+AVQ Sbjct: 300 TAPIRAKYGAPYADLIKRIEAVQ 322 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: 358 Number of extensions: 12 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: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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