Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate RR42_RS07835 RR42_RS07835 membrane protein
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Cup4G11:RR42_RS07835 Length = 434 Score = 256 bits (653), Expect = 1e-72 Identities = 150/399 (37%), Positives = 226/399 (56%), Gaps = 7/399 (1%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 +++ S S+GN +EW+D VY F++ + FFP D LL T F V F MRP+G Sbjct: 27 RAVISASIGNALEWFDLVVYGFFAVTISALFFPNHDENTSLLLTLGTFGVSFFMRPLGAV 86 Query: 86 LMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVGGE 145 ++G+YADR GR+AAL S+ LM G+LIIAL P Y IGV API +V AR++QG S GGE Sbjct: 87 VIGVYADRKGRRAALTLSILLMMVGTLIIALLPTYAAIGVMAPIGIVLARMIQGFSAGGE 146 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRIPF 205 +G++ +L+E A RRGF+SSFQ + L+A G VL TLT +Q+ WGWR+PF Sbjct: 147 FGSATAFLAEHA-PNRRGFYSSFQVASQGLTTLLAAGFGAVLTTTLTPDQMQSWGWRVPF 205 Query: 206 AIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKE-LMTVVGLTMGGTLAFY 264 G L VA Y+RR ++ET F + E + ++ +R L H KE L+ +G+ + T++ Y Sbjct: 206 LFGLLIGPVAYYIRRHVDETPEFLQAE-TTDTPLRDTLSHQKERLLLAMGVVIVATVSTY 264 Query: 265 TYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFGILGT 324 YM Y V +G+ S + + AT + M P++G SD+ GR P + +L Sbjct: 265 -LVLYMPTYAVKQLGLPPSAAFAATLATGVVQMLFAPLVGHWSDRYGRIPPMRLAALL-L 322 Query: 325 LFTVPILTTLHTIQTWWGAFFLIMAAL-IIVSGYTSINAVVKAELFPTEIRALGVGLPYA 383 L ++ L L + +G + L ++++ Y + +E+FP + R G+ L Y Sbjct: 323 LVSIWPLFWLLSHYPGFGVMLAVQVVLGLMMTLYFGALPALASEIFPVKTRTTGLSLSYN 382 Query: 384 LTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAVSL 421 + V++FGG A +I W + G + +Y+ C VSL Sbjct: 383 IAVTLFGGFAPFILTWLISATGSKLAPSFYLMVCAVVSL 421 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: 522 Number of extensions: 34 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: 439 Length of database: 434 Length adjustment: 32 Effective length of query: 407 Effective length of database: 402 Effective search space: 163614 Effective search space used: 163614 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 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