Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_041936398.1 RL_RS17010 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_000009265.1:WP_041936398.1 Length = 437 Score = 186 bits (471), Expect = 2e-51 Identities = 137/436 (31%), Positives = 208/436 (47%), Gaps = 26/436 (5%) Query: 9 LGSAAVPAKEKTTA-SRIKSIFSGSVGNMVEWYDWYVYA-AFSLYFAKAFFPKGDTTAQL 66 + ++ PA T S + + + VG +E++D+YVYA A L F FFP DT A Sbjct: 5 ISASPTPASNSTQVNSPARVLIASLVGTTIEFFDFYVYATAAVLVFPHLFFPASDTNAAT 64 Query: 67 LNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVG 126 L + F++ F RPIG + G + DR GRKA L+A++ M +++I + PGY+ IG+ Sbjct: 65 LQSLVTFSIAFFARPIGAVVFGHFGDRIGRKATLVAALMTMGLSTVLIGMLPGYDAIGIA 124 Query: 127 APILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIV 186 AP+LL R QGL +GGE+G + +E A +R +++ F + G +++ G ++ Sbjct: 125 APLLLALCRFGQGLGLGGEWGGAVLLATENAPPGKRSWYAMFPQLGAPIGFILSSGFFLI 184 Query: 187 LQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKK-EKSKESAMR---TL 242 L +T++ E D+GWRIPF V LY+R + ET F K EK + A+ Sbjct: 185 LAETMSNEDFLDYGWRIPFIASLALVAVGLYVRLKIAETPEFRKAVEKHERVAVPIEVVF 244 Query: 243 LRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNT-----VGMSISDSTTISAATLFLFM 297 H + L+ + + + FY T + + +G S + + F Sbjct: 245 RNHLRSLILGTFIAVATFVLFYLMTVFTLSWGTTPLEKGGLGYSREQFLVVQLVGVVFFG 304 Query: 298 CLQPIIGGLSDKVGRRPIL----IAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALII 353 P+ G LSD RR IL IA I G F +LT+ T GAF + L + Sbjct: 305 LTIPLSGWLSDLYSRRIILTLTTIAIAIFG-FFYATLLTSGLT-----GAFLCSIIGLAL 358 Query: 354 VS-GYTSINAVVKAELFPTEIRALGVGLPYALTVSIFGGT-AEYIALWFKSIGMETGYYW 411 + Y I A + A FPT +R G + + L IFG + A YIA W + Y Sbjct: 359 MGFTYGPIGAALAAP-FPTTVRYTGASMTFNLG-GIFGASLAPYIATWL-ATHYSLDYVG 415 Query: 412 YVTACIAVSLLVYVTM 427 Y A AV LV + + Sbjct: 416 YYLAASAVISLVCIRL 431 Lambda K H 0.325 0.138 0.414 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: 30 Number of successful extensions: 5 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: 439 Length of database: 437 Length adjustment: 32 Effective length of query: 407 Effective length of database: 405 Effective search space: 164835 Effective search space used: 164835 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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