Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_011427276.1 RHE_RS20930 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_000092045.1:WP_011427276.1 Length = 628 Score = 203 bits (516), Expect = 1e-56 Identities = 116/358 (32%), Positives = 188/358 (52%), Gaps = 11/358 (3%) Query: 21 TASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMR 80 T K IF+ S+G + EWYD+Y+Y + + Y +F + + + T FA GFL+R Sbjct: 16 TGEEKKVIFASSLGTVFEWYDFYLYGSLATYIGATYFTQYPEATRNIFTLLAFAAGFLVR 75 Query: 81 PIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGL 140 P G + G D GRK + ++ +M + ++ + P +IG+ API+L+ RLLQGL Sbjct: 76 PFGALVFGRLGDLVGRKYTFLVTILIMGMSTFLVGILPGAASIGIAAPIILIGLRLLQGL 135 Query: 141 SVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWG 200 ++GGEYG +ATY++E A RRG+F+S+ T G ++L V+I++Q + Q AWG Sbjct: 136 ALGGEYGGAATYVAEHAPNGRRGYFTSWIQTTATLGLFLSLIVIILVQSLMAPAQFAAWG 195 Query: 201 WRIPFAIGALCAVVALYLRRGMEETESFTKKEKSKESAMRTLL------RHPK-ELMTVV 253 WRIPF + + +++++R M E+ +F + + + + L ++ K L+ ++ Sbjct: 196 WRIPFLVSVVLLGISVWIRLKMNESPAFQRMKAEGKGSKAPLTEAFGQWKNAKIALIALL 255 Query: 254 GLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRR 313 G TMG + +Y Y +L N + + + + + A LFL + GGLSDKIGR+ Sbjct: 256 GATMGQAVVWYGGQFYALFFLQNVLKVDLFSANVMVAIALFLGTPFFVIFGGLSDKIGRK 315 Query: 314 PILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPT 371 PI++A G L L TW L A I + T+ A K + PT Sbjct: 316 PIIMA----GLLIAAVTYNPLFKAMTWTANPALAEAQASIRATVTADPADCKFQFNPT 369 Score = 40.4 bits (93), Expect = 2e-07 Identities = 26/98 (26%), Positives = 42/98 (42%), Gaps = 1/98 (1%) Query: 340 WWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALW 399 W G ++ ++ V+ A + ELFPT IR G+ LPY + FGG A Sbjct: 527 WVGTVAILFVLVLYVTMVYGPIAALLVELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFA 586 Query: 400 FKSIGMETGY-YWYVTACIAVSLLVYITMKDTRKHSRI 436 + + Y WY A++L++ + K+ I Sbjct: 587 MSAAAGDIYYGLWYPIVFAAITLVIGVIFLPETKNRDI 624 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: 732 Number of extensions: 40 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 439 Length of database: 628 Length adjustment: 35 Effective length of query: 404 Effective length of database: 593 Effective search space: 239572 Effective search space used: 239572 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: 52 (24.6 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