Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_057508837.1 ABB28_RS11900 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_001431535.1:WP_057508837.1 Length = 408 Score = 200 bits (509), Expect = 6e-56 Identities = 122/373 (32%), Positives = 188/373 (50%), Gaps = 8/373 (2%) Query: 32 SVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWLMGLYA 91 ++ +VEWYD+ +Y F+ ++VFF G+T LL T A FAV +LMRP+G G Sbjct: 5 ALSTVVEWYDFTLYLYFATVLSRVFFGGGETA--LLATLAGFAVSYLMRPLGALCFGHLG 62 Query: 92 DRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGEYGTSAT 151 DR GR+ L+AS+ LM L AL P+Y IG A +LL+ R + SVGGEY Sbjct: 63 DRLGRRWMLLASMALMAAAMLATALLPTYAQIGASAGVLLLALRCVMAFSVGGEYTGVVA 122 Query: 152 YLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGWRIPFAIGALC 211 YL E A RRG +S G L+A+ + + L L WGWRIPF +GA Sbjct: 123 YLLESAPPRRRGLVTSLASAASEVGALLAVALSALTVALLPAPALDTWGWRIPFFVGAGL 182 Query: 212 AVVALYLRRGMEETESFTKKEKS---KESAMRTLLR-HPKELMTVVGLTMGGTLAFYTYT 267 A++ L R GM E+ F ++++ + +R +LR HP + ++ G++ +Y Sbjct: 183 ALLILLARSGMHESPEFERQQREGSVPSAPIRQILRSHPGAVARTFAISALGSITYYVGI 242 Query: 268 TYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPILIAFGILGTLFT 327 TY+ +L + G ++ +S + P+ G LSD+ GRRP+L+ +L L Sbjct: 243 TYVPAFL-HANGRGEGEALWLSTIAAVAVILATPLFGLLSDRFGRRPLLLGLTLLSALLP 301 Query: 328 VPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALTVS 387 + + + T G + + G +++ A AE FP E R G+ L + + Sbjct: 302 LSMFGWMAQAST-MGVIGAAVVLACVAGGISAVAASATAEQFPGEGRLSGLALGVTMATA 360 Query: 388 IFGGTAEYIALWF 400 IFGG ++A W+ Sbjct: 361 IFGGATPWLAQWW 373 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: 484 Number of extensions: 24 Number of successful extensions: 6 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: 408 Length adjustment: 32 Effective length of query: 407 Effective length of database: 376 Effective search space: 153032 Effective search space used: 153032 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: 50 (23.9 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