Align TRAP dicarboxylate transporter, DctP-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate AZOBR_RS19865 AZOBR_RS19865 ABC transporter substrate-binding protein
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__azobra:AZOBR_RS19865 Length = 362 Score = 450 bits (1158), Expect = e-131 Identities = 218/355 (61%), Positives = 256/355 (72%), Gaps = 1/355 (0%) Query: 1 MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60 M RRSFL A +G AA+TLA PA+AQS P+V WRL SSFPKSLDTIYG A+V+S+ V+ Sbjct: 1 MKRRSFLASAGVG-VAASTLAAPAIAQSTPEVHWRLASSFPKSLDTIYGAADVISRRVAA 59 Query: 61 ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120 +D F I+ FA+ EIVPGLQ DA GTVE HT YYY GKDP + A VPFGL+A Sbjct: 60 ITDNKFTIRPFASGEIVPGLQVLDAVQNGTVECGHTASYYYVGKDPTFTFDATVPFGLNA 119 Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180 R NAW GGG++L EF ++ FP GNTG QMGGWFRKEI TV DLSGLK R+GG Sbjct: 120 RQQNAWILQGGGMELLREFFKGYNVVNFPAGNTGTQMGGWFRKEIKTVQDLSGLKFRIGG 179 Query: 181 FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWWE 240 FAG+V+ KLG+VPQQ+AGGDIYP+LEKGT+DA EW+GPYDDEKLGF KVA YYYYPGWWE Sbjct: 180 FAGQVLTKLGVVPQQIAGGDIYPSLEKGTIDAAEWIGPYDDEKLGFNKVAKYYYYPGWWE 239 Query: 241 GGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLRP 300 GG V + N+ +E LPK YQA L AC A M KYD NP ALK LVA GAQLRP Sbjct: 240 GGLNVSLLVNQQKWEELPKPYQAALEAACYEALAIMNAKYDADNPAALKRLVAGGAQLRP 299 Query: 301 FSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTF 355 F +E++EAC+ AA E+Y E NP F KIY+ FR + YLW +VAE ++D F Sbjct: 300 FPREVMEACYKAAYELYDETAKNNPEFAKIYEPWKKFRDEEYLWFRVAENSFDNF 354 Lambda K H 0.319 0.134 0.417 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: 441 Number of extensions: 15 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: 365 Length of database: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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