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 AZOBR_RS19240 AZOBR_RS19240 ABC transporter substrate-binding protein
Query= TCDB::D5ALT6 (365 letters) >FitnessBrowser__azobra:AZOBR_RS19240 Length = 364 Score = 419 bits (1076), Expect = e-122 Identities = 197/359 (54%), Positives = 255/359 (71%) Query: 1 MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60 M RRSFL A +G AA+T +A PA+AQS P++ WR+ SS+PKSLDTI+GGAE++++ V+ Sbjct: 1 MKRRSFLASAGVGLAASTVVAAPAIAQSQPEIKWRMASSYPKSLDTIFGGAELIARRVAA 60 Query: 61 ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120 A+D FQI+ FAA EIVP LQ DA GT+E + Y+Y GKDP + A+PFGL+ Sbjct: 61 ATDNKFQIRTFAAGEIVPALQVLDAVQNGTIECGQSAAYFYIGKDPTFCFDTAMPFGLNT 120 Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180 R +W HGGG++L E + P GNT AQMGGWFRKEI TV DLSGLKMRVGG Sbjct: 121 RQHISWMMHGGGLELMRELFREHNIYNIPAGNTTAQMGGWFRKEIKTVEDLSGLKMRVGG 180 Query: 181 FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWWE 240 AG++M KLGLVPQQ+ GGDIYPALE+GT+DA E+VGPYDDEKLGF+KVA YYY PGWWE Sbjct: 181 LAGQIMGKLGLVPQQIGGGDIYPALERGTIDAAEFVGPYDDEKLGFHKVAKYYYSPGWWE 240 Query: 241 GGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLRP 300 G + M N A+E LP++Y+ +L AC + M+ KYD N ALK LVA GAQLR Sbjct: 241 GSAQIPLMINITAWEQLPESYKTILEQACWEANTWMIAKYDAVNAAALKRLVAGGAQLRA 300 Query: 301 FSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMMIQ 359 F ++++ AC A E+Y E++A NP FKK+Y++ FR + LW +VAE ++D+++ Q Sbjct: 301 FPRDVMMACEKIANELYDELSAKNPRFKKVYEAWKPFRDEERLWFRVAENSFDSYVYSQ 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: 421 Number of extensions: 19 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: 364 Length adjustment: 29 Effective length of query: 336 Effective length of database: 335 Effective search space: 112560 Effective search space used: 112560 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