Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate 8501405 DvMF_2135 TRAP dicarboxylate transporter, DctP subunit (RefSeq)
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__Miya:8501405 Length = 365 Score = 139 bits (350), Expect = 1e-37 Identities = 88/284 (30%), Positives = 151/284 (53%), Gaps = 6/284 (2%) Query: 8 LLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITFKMFAGGV 67 L A+LP A ++A ++ A + G V + + LE+ S+G + G Sbjct: 44 LAAILPGWPRTA--SAATELTLAVVTTPGSAQHVCAERFRQLLEERSHGAYRVVVHHSGT 101 Query: 68 LGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIIDGEIGQEI 127 LG+E E+++Q Q+G VQ+ ++LG++ P VP+V V + PF+FRD +++DG G+ + Sbjct: 102 LGTETEILQQLQLGGVQLAIITLGVLDPFVPEVKVLDYPFLFRDAAEADRVLDGATGRAL 161 Query: 128 LDKITNSDFNLVALAWMDGGSRSIYTK-KPVRSLEDLKGMKIRVQGNPLFIDMMNAMGGN 186 LD + L L + + G R + +PVRS++D++G+KIRV + L ++ A+G N Sbjct: 162 LDALER--VGLKGLHFSENGFRHLTNNVRPVRSVDDVRGLKIRVLESTLHRELWRALGAN 219 Query: 187 GIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVMSKTTWN 246 M I++ LQ G IDG EN + E+ + KY +LTGH+ + + +N Sbjct: 220 PTPMG-WPIYAELQQGTIDGQENPLWVMAEYRMPEVQKYLSLTGHVYSAHADLANLAWFN 278 Query: 247 KLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFI 290 L P ++ LV + +A +RA K A +L+ AG++ + Sbjct: 279 GLPPAERTLVMQCMADAAAYQRAYNRQKDADYLRRLREAGMQVV 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: 205 Number of extensions: 7 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: 323 Length of database: 365 Length adjustment: 29 Effective length of query: 294 Effective length of database: 336 Effective search space: 98784 Effective search space used: 98784 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