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_028585283.1 G494_RS0115715 C4-dicarboxylate ABC transporter
Query= TCDB::Q8YSQ7 (445 letters) >NCBI__GCF_000429965.1:WP_028585283.1 Length = 439 Score = 394 bits (1011), Expect = e-114 Identities = 198/432 (45%), Positives = 290/432 (67%), Gaps = 9/432 (2%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70 V+F+G + G+P AF LGGVA LFG +G ++ +F+ R+FG+M NYTLLA Sbjct: 13 VLFSGIFL----GFPTAFVLGGVAFLFGANIMGPDIYG-LFIA----RLFGLMKNYTLLA 63 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 +P F+FMG +EKSG+AERL M IL GR RGGL ++ + + A+ AA TGVV A+ + + Sbjct: 64 VPLFLFMGVFMEKSGMAERLFNAMHILWGRFRGGLGISTIAISAVFAAATGVVGASEITI 123 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 GL++LP+ML YN+ +A G I A GTLG +IPPSV+++V G ISVG LF+G ++PG Sbjct: 124 GLMALPVMLAKKYNRSMACGAICAGGTLGILIPPSVMIIVYGPIARISVGKLFLGCLLPG 183 Query: 191 LMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIF 250 +++ + ++ I ++ P LP + R+ + + ++ ++PP ++IL VLGSIF Sbjct: 184 ILLTLLYMAYIGIRCYLNSADGPPLPPEERQGSVREKFRILLTSVLPPALIILSVLGSIF 243 Query: 251 FGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLVF 310 FG A TEA AVG ++ALAA+ + LR+ C+ TL IT+M++ I +G+T FS VF Sbjct: 244 FGIAAVTEAAAVGAVASMALAASYRRLNFAVLREACEQTLTITAMIMMIAVGATFFSTVF 303 Query: 311 RGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLGI 370 L GD+ + + NLP GK G L M + G FID+ I FI++PL P+A +LG Sbjct: 304 VALGGDEVITGMFINLPMGKWGILATIMLLLVFCGMFIDWMGILFIIVPLITPIAAELGF 363 Query: 371 DLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLLI 430 D VW+ V++ NLQ SFLTPPF +++FYL+G+APPEV T+DIYRGV+PF+ LQ+ +LL+ Sbjct: 364 DPVWFAVLVMVNLQISFLTPPFAYSIFYLKGIAPPEVETADIYRGVMPFVGLQVFAILLL 423 Query: 431 IIFPGIVSFLPS 442 I+FP I+++LP+ Sbjct: 424 ILFPEIITWLPN 435 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: 571 Number of extensions: 24 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: 439 Length adjustment: 32 Effective length of query: 413 Effective length of database: 407 Effective search space: 168091 Effective search space used: 168091 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