Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_013088471.1 BC1002_RS02340 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >NCBI__GCF_000092885.1:WP_013088471.1 Length = 425 Score = 248 bits (634), Expect = 2e-70 Identities = 140/401 (34%), Positives = 221/401 (55%), Gaps = 5/401 (1%) Query: 26 KSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85 +++ + S+GN +EW+D VY F++ +K+FFP G+ T LL T F V F MRP+G Sbjct: 18 RAVVAASIGNALEWFDLVVYGFFAVTISKLFFPAGNDTVSLLLTLGTFGVSFFMRPLGAI 77 Query: 86 LMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGE 145 ++G Y+DRAGRK AL S+ LM G+LIIA+ P+Y++IG+ AP++LV ARL+QG S GGE Sbjct: 78 VIGAYSDRAGRKAALTLSIMLMMGGTLIIAILPTYQSIGLAAPLILVLARLMQGFSAGGE 137 Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGWRIPF 205 +G++ +L+E RRGF++S+Q + L+A G +L L+ EQ+ +WGWR+PF Sbjct: 138 FGSATAFLAE-HEPGRRGFYASWQMASQGLTTLLAAGFGALLTGGLSPEQMTSWGWRVPF 196 Query: 206 AIGALCAVVALYLRRGMEETESFTKKEKSKESAMRTLLRHPKELMTVVGLTMGGTLAFYT 265 G L VA Y+R ++ET F E ++ T L+ +G+ + GT++ Y Sbjct: 197 FFGLLIGPVAFYIRTKLDETPEFLAAETTQTPLRDTFATQKLRLVIAMGVVILGTVSSY- 255 Query: 266 YTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPILIAFGILGTL 325 +M Y V +G++ S + + A T + M PV G SD GR I++ +L + Sbjct: 256 LMLFMPTYGVRQLGLAPSVAFSAIAVTGLIQMVFSPVAGHWSDLHGRTRIMLGAAVLLFV 315 Query: 326 FTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPYALT 385 P L ++ + +VSGY + +E+FP + R G+ L Y + Sbjct: 316 LVYPAFAFLIAHPSFGTLIVWQIVFGFLVSGYFGATPGLLSEIFPVQTRTTGMSLAYNIA 375 Query: 386 VSIFGGTAEYIALWFKSI---GMETGYYWYVTACIAVSLLV 423 V+IFGG +I W S+ YY A ++++ L+ Sbjct: 376 VTIFGGFGPFIIAWLISVTGSKAAPSYYVMFAALLSIAALI 416 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: 545 Number of extensions: 30 Number of successful extensions: 3 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: 425 Length adjustment: 32 Effective length of query: 407 Effective length of database: 393 Effective search space: 159951 Effective search space used: 159951 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