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_020922288.1 RHE_RS18500 TRAP transporter large permease subunit
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_000092045.1:WP_020922288.1 Length = 497 Score = 470 bits (1210), Expect = e-137 Identities = 233/430 (54%), Positives = 317/430 (73%) Query: 10 PVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLL 69 P MF G ++ + G+PVAFSL V + FG++GI G F FL A+P R FGI++N LL Sbjct: 9 PAMFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFGIVSNDLLL 68 Query: 70 AIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVA 129 AIP+F MGA+LE+ G+AE LLE G L G + GGLA AV+LVGA+L A TG VAA+V+ Sbjct: 69 AIPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVIT 128 Query: 130 MGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIP 189 MG+ISLPIMLRYGY+ LATGVIAASGT+ Q+IPPS+VLVVL DQLG SVGD+++G++ P Sbjct: 129 MGVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGP 188 Query: 190 GLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSI 249 ++ + F L VL+++ +RP P LP +VR AL +V+ M+P ++LI LVLG+I Sbjct: 189 SILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVLIFLVLGTI 248 Query: 250 FFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLV 309 F G ATPTEAGA+G GA+ LAA N + T +R+ +T ITSMVV ILIGST FSLV Sbjct: 249 FMGLATPTEAGALGVVGAMLLAAMNRRLTWPLIREAMTSTTHITSMVVMILIGSTCFSLV 308 Query: 310 FRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLG 369 F+G++G +++ +L+ +PGG +GFL +F+L FF+DFFEIAFIVIP+ PVA LG Sbjct: 309 FQGMDGSRWIEHMLSGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLG 368 Query: 370 IDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLL 429 IDL+W+GV++ N+QTSF+ PPFGFALFYLR +A +V TSDIY G +P++ +Q++++ + Sbjct: 369 IDLIWFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVGMQIILVAI 428 Query: 430 IIIFPGIVSF 439 +I +P V++ Sbjct: 429 VIFWPQSVTY 438 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: 745 Number of extensions: 30 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: 445 Length of database: 497 Length adjustment: 33 Effective length of query: 412 Effective length of database: 464 Effective search space: 191168 Effective search space used: 191168 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 Apr 09 2024. 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