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 RR42_RS20415 RR42_RS20415 ABC transporter substrate-binding protein
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__Cup4G11:RR42_RS20415 Length = 377 Score = 423 bits (1087), Expect = e-123 Identities = 210/371 (56%), Positives = 247/371 (66%), Gaps = 16/371 (4%) Query: 1 MDRRSFLTKAAIGGA----------------AATTLATPALAQSMPKVTWRLTSSFPKSL 44 M+RRSFL KA+ A AA + PA+ S P V WRL SSFPKSL Sbjct: 1 MERRSFLLKASAVAATGALAACGKEEKAAAPAAAGASAPAVIGSNPAVEWRLASSFPKSL 60 Query: 45 DTIYGGAEVLSKMVSEASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGK 104 DTIYGGAE+LS+ V E +DG F I+VFAA E+VPGLQ D+ TV+ HT GYYY+GK Sbjct: 61 DTIYGGAELLSQRVKELTDGKFNIKVFAAGELVPGLQVLDSVQNNTVQIGHTAGYYYFGK 120 Query: 105 DPAWALGAAVPFGLSARGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKE 164 +P VPFGL++R NAW G G+ L EF ++ F GGNT AQMGGWFRKE Sbjct: 121 NPTLCFDTTVPFGLTSRQQNAWMMQGNGMKLMREFFKEYNVVNFLGGNTNAQMGGWFRKE 180 Query: 165 INTVADLSGLKMRVGGFAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKL 224 I TVADL GLK R+ GFAG V+ +LG+VPQQ+AGGDIYPALEKGT+DA EWVGPYDDEKL Sbjct: 181 IKTVADLQGLKYRIAGFAGVVLSRLGVVPQQIAGGDIYPALEKGTIDAAEWVGPYDDEKL 240 Query: 225 GFYKVAPYYYYPGWWEGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKN 284 GFYKVAPYYYYPGWWEG + F + YE LP Y+ L TA +M+ KYD N Sbjct: 241 GFYKVAPYYYYPGWWEGSAQLSFYSSATEYEKLPALYKRALETATIEVHTNMMAKYDTVN 300 Query: 285 PLALKSLVANGAQLRPFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLW 344 P AL L+ NG +LRPFS+EI+EACF A Q+ YAE TA NP+FKKIYD FR + W Sbjct: 301 PQALARLLENGVKLRPFSKEIMEACFKATQDAYAEETAKNPSFKKIYDDWRVFRNNEAAW 360 Query: 345 TQVAEYNYDTF 355 VAE + F Sbjct: 361 FNVAEQAFSQF 371 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: 454 Number of extensions: 16 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: 377 Length adjustment: 30 Effective length of query: 335 Effective length of database: 347 Effective search space: 116245 Effective search space used: 116245 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