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 GFF1984 PGA1_c20180 TRAP transporter, subunit DctP
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__Phaeo:GFF1984 Length = 360 Score = 224 bits (572), Expect = 2e-63 Identities = 125/336 (37%), Positives = 183/336 (54%), Gaps = 5/336 (1%) Query: 1 MDRRSFLTKAAIGG--AAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMV 58 MDRRSFL +A+GG AAATTLA PA AQ K T + +++ + L ++ A+ ++ + Sbjct: 1 MDRRSFLKTSALGGSAAAATTLAAPAYAQG--KRTLTMVTTWGRGLAGVHDSAQYVADAI 58 Query: 59 SEASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGL 118 + S G+ + V AA E+V + DA AG + H YY+ G+ P +A AVPFG+ Sbjct: 59 TAMSGGDLTVDVKAAGELVGAFEVFDAVTAGQADMYHGADYYFTGQHPGYAYFTAVPFGM 118 Query: 119 SARGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRV 178 + + + W YHG G L++E GL F GGNTG Q GGW+ KEI D +GLK R+ Sbjct: 119 TPQELTNWYYHGDGHALHDELGQIFGLKSFIGGNTGPQAGGWYNKEIKGPEDFNGLKFRM 178 Query: 179 GGFAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGW 238 G GK + KLG Q + G ++Y AL G +D TEW+GP+ DEK GF ++ YY G+ Sbjct: 179 PGLGGKALGKLGASVQNIPGSEVYQALSSGAIDGTEWIGPWADEKAGFQEITKTYYTAGF 238 Query: 239 WEGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQL 298 E G + N+ +EGL A+Q ++ A A L ++ N AL+ L + G + Sbjct: 239 HEPGAALSVATNRDVFEGLSPAHQKVIEMASAAGHQWSLAQFMNNNGAALQRLQSGGVKT 298 Query: 299 RPFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSM 334 F + +A +A +E E + F KI S+ Sbjct: 299 LEFPDSVWDAFGSATKETLDEFMG-DELFAKIRGSV 333 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: 348 Number of extensions: 21 Number of successful extensions: 1 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