Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate WP_086511750.1 BZY95_RS20405 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_002151265.1:WP_086511750.1 Length = 464 Score = 442 bits (1138), Expect = e-129 Identities = 232/458 (50%), Positives = 317/458 (69%), Gaps = 26/458 (5%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLG---IGLGV---FDPIFLTAMPQRIFGIMAN 65 +F +L GYPVA +L G A++F LG + +GV F+ + AMP R++GIM N Sbjct: 5 LFLTVCAVLMLGYPVALALAGTALIFAGLGHLLLQMGVPVPFEARMMGAMPNRLYGIMTN 64 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 TLLA+P F+ MG +LEKS +AE LL+ M +L G LRGGL ++V+LVG LLAA+TG+V A Sbjct: 65 QTLLAVPLFVLMGVLLEKSRVAETLLDAMALLFGTLRGGLGISVILVGMLLAASTGIVGA 124 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLG--------- 176 TVV MGL+SLP ML+ GY+ LATG I A+GTLGQIIPPS+ LV+LGD L Sbjct: 125 TVVTMGLLSLPTMLKRGYSPALATGSICATGTLGQIIPPSIALVLLGDVLSNAYQRAQLA 184 Query: 177 --------ISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQV--REIGGK- 225 +SVGDLF+G++IPGL++ A+ +++++VA+++P+ APA V +E+G Sbjct: 185 MGVWSPKTVSVGDLFVGALIPGLLLVVAYIVYMMVVAWLKPESAPAADRDVLKQELGHSG 244 Query: 226 ALGKRVIQVMIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQV 285 ++ +I+ +IPP++LI+ VLGSI GFATPTEA AVG GA LA N + L LR+V Sbjct: 245 SILPLLIKGLIPPVLLIVAVLGSILGGFATPTEASAVGATGAFLLALVNRRMNLPMLREV 304 Query: 286 CDTTLRITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLG 345 TT ++TSMV ILIG+ FSLVFR G++ + ++ LPGG +G V M +FLLG Sbjct: 305 VFTTTKVTSMVFLILIGAALFSLVFRAYGGEELVKEMFEALPGGVVGATLVVMLVIFLLG 364 Query: 346 FFIDFFEIAFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPP 405 F +DF EI F+V+P+ PV +G+D +W G+++ NLQTSFLTPPFGFALFYLRGV P Sbjct: 365 FILDFIEITFVVVPIVGPVLLMMGLDPIWLGIMIAVNLQTSFLTPPFGFALFYLRGVTPE 424 Query: 406 EVTTSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 V TS IYRGV+PFIL+QL +L + +FPG+ ++LPS+ Sbjct: 425 SVPTSAIYRGVVPFILMQLGMLGALALFPGLATWLPSV 462 Lambda K H 0.331 0.149 0.437 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: 617 Number of extensions: 32 Number of successful extensions: 4 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: 445 Length of database: 464 Length adjustment: 33 Effective length of query: 412 Effective length of database: 431 Effective search space: 177572 Effective search space used: 177572 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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