Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_058859649.1 AS188_RS01290 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_001482365.1:WP_058859649.1 Length = 449 Score = 226 bits (576), Expect = 1e-63 Identities = 141/415 (33%), Positives = 215/415 (51%), Gaps = 17/415 (4%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 +++ + ++GN EW+D+ VYA +Y + FFP T L+T FA FL+RP+GG Sbjct: 19 RAVAASAIGNATEWFDYGVYAVSVVYITQNFFPGEYGTILALST---FAFSFLVRPLGGL 75 Query: 86 LMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGE 145 G DR GRKR L ++ LM + I L P+ ETIG+ APILL+ R +QG S GGE Sbjct: 76 FWGPLGDRLGRKRILALTIILMAGATFCIGLLPTVETIGIAAPILLILLRAVQGFSTGGE 135 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVL--QQFLTTEQLYAWGWRI 203 YG +AT+++E A +RRGF SF ++G ALG LIVL + L + + WGWRI Sbjct: 136 YGGAATFMAEYAPDKRRGFLGSFLEFGTLAG--FALGSLIVLLGEVVLGNDAMSEWGWRI 193 Query: 204 PFAIGALCAVVALYLRRGMEETESFTKKEKSKES------AMRTLL-RHPKELMTVVGLT 256 PF + +V LYLR + ++ F + E+S + A++ L+ R+ + ++ + GL Sbjct: 194 PFLLAGPMGLVGLYLRSRLADSPVFQELEESGHTESSAGMALKDLVTRYWRPMLIMTGLV 253 Query: 257 MGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPIL 316 + + YT +YM YL GM+ TI F M + P G LSD++GR+P+ Sbjct: 254 IALNVVNYTLLSYMPTYLEGQTGMANRTVLTIMFVAQFAMMLVIPFAGALSDRVGRKPMW 313 Query: 317 IAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRAL 376 ++G + L WW + L+ + +I+A A +FPT++R Sbjct: 314 YT-SLIGLFVLAIPMYMLMANGFWWALLGFAVLGLLYIPQLATISATFPA-MFPTQVRYA 371 Query: 377 GVGLPYALTVSIFGGTAEYI-ALWFKSIGMETGYYWYVTACIAVSLLVYITMKDT 430 G + Y L ++FGGTA + G +Y+ A V L+ MK+T Sbjct: 372 GFAITYNLATAVFGGTAPLANEALIGATGNPLVPAFYMMAACVVGLVAVRAMKET 426 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: 579 Number of extensions: 34 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: 449 Length adjustment: 32 Effective length of query: 407 Effective length of database: 417 Effective search space: 169719 Effective search space used: 169719 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 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