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 Ac3H11_3567 TRAP transporter solute receptor, unknown substrate 6
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3567 Length = 360 Score = 410 bits (1055), Expect = e-119 Identities = 202/361 (55%), Positives = 244/361 (67%), Gaps = 3/361 (0%) Query: 1 MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60 MDRRS + A I G A A AQ+ + WRL SSFPKSLDTIYGGA+V SK V Sbjct: 1 MDRRSIIKHAGIAGVLAAGAAPAVHAQAA--IRWRLASSFPKSLDTIYGGADVFSKAVKA 58 Query: 61 ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120 S G F+I V A E++P D GTVE CHTV YY++GK+PA+ALG+A+PFG +A Sbjct: 59 MSGGKFEISVHAGGELMPPFGVMDGVQQGTVEMCHTVPYYFYGKNPAFALGSAIPFGFNA 118 Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180 R MNAW HG G L NEF A I F GGNTG QMGGW+RKEI + AD G+KMR+GG Sbjct: 119 RQMNAWMLHGNGRKLMNEFYANYNAISFAGGNTGTQMGGWYRKEIKSPADFKGMKMRLGG 178 Query: 181 -FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWW 239 G+VM+KLG VPQ + GG+IY ALEKGTLDA EWVGPYDD+KLGF KVAP+YYYPGWW Sbjct: 179 GLVGEVMQKLGAVPQSIPGGEIYQALEKGTLDAAEWVGPYDDQKLGFNKVAPFYYYPGWW 238 Query: 240 EGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLR 299 EGGP V F N+ A++GL +A++ A DML KYD NP ALK LVA ++ Sbjct: 239 EGGPEVDFFVNQKAFDGLSAENKAIIEAATNVAHIDMLAKYDALNPTALKQLVAAKTKVL 298 Query: 300 PFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMMIQ 359 PFSQ +++A F A+ EV+AE A +P +KKIY M F+ D LW + AE YDTFM Q Sbjct: 299 PFSQAVMDASFKASMEVFAENDAKSPEWKKIYADMRTFQRDQILWFRFAEARYDTFMSAQ 358 Query: 360 Q 360 + Sbjct: 359 K 359 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: 448 Number of extensions: 14 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: 360 Length adjustment: 29 Effective length of query: 336 Effective length of database: 331 Effective search space: 111216 Effective search space used: 111216 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