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 Dsui_1233 Dsui_1233 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__PS:Dsui_1233 Length = 363 Score = 438 bits (1127), Expect = e-127 Identities = 208/359 (57%), Positives = 255/359 (71%), Gaps = 3/359 (0%) Query: 1 MDRRSFLTKAAIG---GAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKM 57 M+RRSFL KA +G GAAATT++ PA+AQ+ P + WRLTSSFPKSLDT+YGGAEVL+ Sbjct: 1 MERRSFLKKAGVGIAAGAAATTVSAPAIAQTQPTIKWRLTSSFPKSLDTLYGGAEVLANR 60 Query: 58 VSEASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFG 117 + ++G F I+VFA EIVPGLQA DA GTVE CHT YYY GKD +ALG ++PFG Sbjct: 61 LRAMTNGKFDIRVFAGGEIVPGLQALDAVQQGTVECCHTAPYYYVGKDKTFALGCSIPFG 120 Query: 118 LSARGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMR 177 ++AR MNAW Y+GGG L +EF A ++ F GGN+G QMGGWFRKEI + D+ GLKMR Sbjct: 121 MNARQMNAWVYYGGGQKLLDEFYANYNIVSFMGGNSGTQMGGWFRKEIKNLGDIKGLKMR 180 Query: 178 VGGFAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPG 237 V G G V E+LG VPQQ+AGGDIYPALEKGT+DA EWVGPYDDEKLGF+KVA YYYPG Sbjct: 181 VAGLGGTVFERLGAVPQQIAGGDIYPALEKGTIDAAEWVGPYDDEKLGFFKVAKNYYYPG 240 Query: 238 WWEGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQ 297 WWE GP F NK ++ LPK YQ + A + ML +YD+KNP AL L++ G + Sbjct: 241 WWEPGPAFSFYVNKKEWDKLPKEYQEAFQAAAYEANVTMLAEYDHKNPPALSRLLSQGVK 300 Query: 298 LRPFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFM 356 L+ +S EI+ A + AA E+YAE +A NPAFKKIY +R W VA+ D F+ Sbjct: 301 LQKYSDEIMNAAYKAAMEIYAEESAKNPAFKKIYTEYDKYRKTQNAWFSVADTTMDRFL 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: 460 Number of extensions: 20 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: 363 Length adjustment: 29 Effective length of query: 336 Effective length of database: 334 Effective search space: 112224 Effective search space used: 112224 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