Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_078716023.1 B5D49_RS00840 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_900167125.1:WP_078716023.1 Length = 409 Score = 210 bits (535), Expect = 6e-59 Identities = 125/382 (32%), Positives = 203/382 (53%), Gaps = 10/382 (2%) Query: 33 VGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWLMGLYAD 92 +GN++EWYD+ +Y + ++ FFP D TA L+ T +FA GF+MRP+G L G D Sbjct: 1 MGNIMEWYDFALYGFMASILSQQFFPSEDKTASLMATYGVFAAGFIMRPLGSALFGWLGD 60 Query: 93 RAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGEYGTSATY 152 GR + ++ SV LM F ++++ L P+Y +IG+ API LV RLLQGLSVGGE+ +S TY Sbjct: 61 TIGRSKVMLISVVLMTFPTVLLGLLPTYHSIGIWAPIFLVVIRLLQGLSVGGEFSSSVTY 120 Query: 153 LSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGWRIPFAIGALCA 212 L E + + +RG SF V + G L+ G+ + T+EQL +W WR+PF + L Sbjct: 121 LVETSPENQRGLSGSFANVGSLGGMLLGSGMAALTSLVFTSEQLNSWAWRLPFFVAGLLG 180 Query: 213 VVALYLRRGMEETESFTK--KEKSKESAMRTLLR-HPKELMTVVGLTMGGTLAFYTYTTY 269 + A+ LR+G+ ++ FTK K + K+S +R +L + K+++ V FY Y Sbjct: 181 IGAIVLRQGLPNSKQFTKHAKGRDKDSPLREVLTVNRKQMIQGVLFASAYGAVFYLGLVY 240 Query: 270 MQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPILIAFGILGTLFTVP 329 + +L + ++ + + A L + PV +SDK RR L+ G +F Sbjct: 241 IPTWLKEYGQVPLAQAQDWNTAATALTLAALPVAAWVSDKFFRRTHLLVLA-FGGIFV-- 297 Query: 330 ILTTLHTIQTWWGAFFLIMAALI---IVSGYTSINAVVKAELFPTEIRALGVGLPYALTV 386 + LH+ + ++ L+ +++ + + ELFP R G + + L + Sbjct: 298 LAWPLHSWMLGGTGTSVTISQLVFGLLLAVPCGVAPALFVELFPAGDRLSGYSIAFNLGM 357 Query: 387 SIFGGTAEYIALWFKSI-GMET 407 + GG+ +A W I G+ET Sbjct: 358 GVVGGSTPMLATWLVQITGLET 379 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: 552 Number of extensions: 24 Number of successful extensions: 2 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: 409 Length adjustment: 32 Effective length of query: 407 Effective length of database: 377 Effective search space: 153439 Effective search space used: 153439 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