Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate RR42_RS19610 RR42_RS19610 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__Cup4G11:RR42_RS19610 Length = 432 Score = 269 bits (687), Expect = 1e-76 Identities = 156/422 (36%), Positives = 239/422 (56%), Gaps = 12/422 (2%) Query: 18 ERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGF 77 E + A R K+I + ++GN +EW+D+ VY+ F+L AK+FFP G+ L T A F VGF Sbjct: 6 EISKAQRRKAILAATIGNGLEWFDFTVYSFFALIIAKLFFPTGNDLTSFLLTVATFGVGF 65 Query: 78 LMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLL 137 MRP+G ++G+YADR GRK AL ++ +M G+ II L+P+Y +IG+ AP L+V ARL+ Sbjct: 66 FMRPVGAIVLGVYADRVGRKAALTLTILMMALGTAIIGLAPTYSSIGLWAPALIVLARLI 125 Query: 138 QGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTL-ISGQL-IALGVLIVLQQFLTTEQ 195 QG S GGE G + +L E A E RG ++S+Q + IS L A+G L++ L EQ Sbjct: 126 QGFSAGGEVGGATAFLIEHAPDEERGAYASWQQASQGISFMLGAAMGALVI--NGLEPEQ 183 Query: 196 LYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKK------EKSKESAMRTLLR-HPKE 248 + AWGWRIPF G L V +Y+R +EE +F + K K S + +LR HP+E Sbjct: 184 IDAWGWRIPFLFGLLIGPVGMYIRSHLEEPPAFEARRAERAASKVKFSPLTQVLRDHPRE 243 Query: 249 LMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSD 308 ++ +G+T+ T+ Y YM Y +G+ + + +A + + L P++G LSD Sbjct: 244 VLAGLGVTILWTVCTYVLVFYMPSYAKQQLGLPLGATFQSTALCGAIILVLCPLMGMLSD 303 Query: 309 KIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAEL 368 ++GR+ +L ++ + P+ L+ T + + I+++ +T V AE Sbjct: 304 RVGRKRMLGTVALIIGVLAYPLFHWLNVSPTTQTLLMVQVILGILLAAFTGPAPAVLAEQ 363 Query: 369 FPTEIRALGVGLPYALTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAVSLLVYITM 427 FPTE+R+ G+ L Y V+IFGG A I W S G + +YV A A+S + + M Sbjct: 364 FPTEVRSTGLSLAYNFAVTIFGGFAPLIVTWLIASSGSKLAPAYYVIAAAAISFVALLFM 423 Query: 428 KD 429 D Sbjct: 424 HD 425 Lambda K H 0.326 0.138 0.416 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: 530 Number of extensions: 30 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: 432 Length adjustment: 32 Effective length of query: 407 Effective length of database: 400 Effective search space: 162800 Effective search space used: 162800 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 (21.7 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