Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate CA265_RS22390 CA265_RS22390 alpha-ketoglutarate transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Pedo557:CA265_RS22390 Length = 428 Score = 562 bits (1448), Expect = e-165 Identities = 275/421 (65%), Positives = 339/421 (80%), Gaps = 2/421 (0%) Query: 19 KTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFL 78 K R+KSIF GSVGN+VEWYDWY Y+AF+LYF+ AFFP + TAQLL+TA IFAVGFL Sbjct: 7 KDVEYRLKSIFGGSVGNLVEWYDWYTYSAFALYFSPAFFPNSNPTAQLLDTAGIFAVGFL 66 Query: 79 MRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQ 138 MRPIGGWL G AD+ GRK ++ SV +M GSLII L+PGY+ IG+ AP+LL+FARL+Q Sbjct: 67 MRPIGGWLFGSIADKLGRKRSMTLSVLIMAIGSLIIGLTPGYKQIGIAAPLLLIFARLIQ 126 Query: 139 GLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ-TLTTEQLY 197 GLS GGEYGTSATYLSEMATK+ RGF+SSFQYVTLI GQL+ALG+ ++LQ LT +L+ Sbjct: 127 GLSTGGEYGTSATYLSEMATKKHRGFYSSFQYVTLIGGQLLALGIQLILQNWLLTPAELH 186 Query: 198 DWGWRIPFAIGALCAIVALYLRRGMEETESF-AKKEKSKESAMRTLLRHPKELMTVVGLT 256 +WGWRIPF IGA+ + +ALYLRR ++ET +F +K K+ + L+++PKE+ TVVGLT Sbjct: 187 EWGWRIPFFIGAILSFIALYLRRHIDETSAFKSKNTADKKGGIAVLMKYPKEVFTVVGLT 246 Query: 257 MGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPIL 316 +GGT+AFYT++TYMQK+LVNTV +S STT+S +L +F+ LQP+ G LSDK+GR+P+L Sbjct: 247 LGGTIAFYTFSTYMQKFLVNTVHLSKETSTTLSFISLLVFVVLQPLFGLLSDKIGRKPLL 306 Query: 317 IAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRAL 376 I FG+LGTL T PILT L F L++ ALIIVSGYTSINAVVKAELFP EIRAL Sbjct: 307 IGFGVLGTLCTYPILTGLAGESNTTIIFLLMIGALIIVSGYTSINAVVKAELFPAEIRAL 366 Query: 377 GVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSRI 436 GVGLPYALTV+IFGGTAEY ALWFK+IG E +YWYVT CI +SL++Y TMKDT+ HS+I Sbjct: 367 GVGLPYALTVAIFGGTAEYFALWFKNIGHENYFYWYVTGCILISLILYTTMKDTKHHSKI 426 Query: 437 E 437 E Sbjct: 427 E 427 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: 726 Number of extensions: 44 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: 428 Length adjustment: 32 Effective length of query: 407 Effective length of database: 396 Effective search space: 161172 Effective search space used: 161172 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