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 SMc04251 SMc04251 mannitol-binding periplasmic signal peptide protein
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__Smeli:SMc04251 Length = 368 Score = 628 bits (1619), Expect = 0.0 Identities = 299/368 (81%), Positives = 331/368 (89%), Gaps = 3/368 (0%) Query: 1 MDRRSFLTKAAIGG---AAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKM 57 MDRRSF+ A+IGG AAA+ LA PA+AQ+ PKVTWRLTSSFPKSLDTIYGGAEVLSK Sbjct: 1 MDRRSFIKHASIGGLGAAAASALAAPAIAQTNPKVTWRLTSSFPKSLDTIYGGAEVLSKY 60 Query: 58 VSEASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFG 117 VSEA+DGNFQIQVFAA EIVPGLQAADA AAGTVEACHTV YYYWGKDP WALGAAVPF Sbjct: 61 VSEATDGNFQIQVFAAGEIVPGLQAADAAAAGTVEACHTVAYYYWGKDPTWALGAAVPFA 120 Query: 118 LSARGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMR 177 L+ARGMNAW YHGGGIDL+NEFL TQGL+G+PGGNTG QMGGWFRKEI TVAD+ GLKMR Sbjct: 121 LNARGMNAWHYHGGGIDLFNEFLGTQGLVGYPGGNTGVQMGGWFRKEIKTVADMKGLKMR 180 Query: 178 VGGFAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPG 237 VGGFAGKVME+LG+VPQQ+AGGDIYPALEKGT+DA EWVGPYDDEKLGFYKVAPYYYYPG Sbjct: 181 VGGFAGKVMERLGVVPQQLAGGDIYPALEKGTIDAAEWVGPYDDEKLGFYKVAPYYYYPG 240 Query: 238 WWEGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQ 297 WWEGGPTVH MFNKAA++GLPKAYQ+LLRTACQA DA+MLQKYDY NP A+K LVA GA+ Sbjct: 241 WWEGGPTVHAMFNKAAFDGLPKAYQSLLRTACQATDANMLQKYDYLNPSAIKRLVAAGAK 300 Query: 298 LRPFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMM 357 L PFS EIL ACF+ + +VYAEM A+N FKKI++S+ AFRA+++L Q+AEYNYDTFMM Sbjct: 301 LSPFSPEILSACFDESNKVYAEMEASNAPFKKIWESIKAFRAEYFLNAQIAEYNYDTFMM 360 Query: 358 IQQRNGKI 365 IQQRNGKI Sbjct: 361 IQQRNGKI 368 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: 531 Number of extensions: 18 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: 368 Length adjustment: 30 Effective length of query: 335 Effective length of database: 338 Effective search space: 113230 Effective search space used: 113230 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