Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate BPHYT_RS27905 BPHYT_RS27905 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__BFirm:BPHYT_RS27905 Length = 435 Score = 458 bits (1178), Expect = e-133 Identities = 229/432 (53%), Positives = 307/432 (71%), Gaps = 5/432 (1%) Query: 1 MDNSQTLPLGSAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKG 60 M + L +A P + + S ++SI GS+GN++EWYD++VY FS++FA +FFP+ Sbjct: 1 MHETTPAELDAATRPLRRR---SALRSIAGGSIGNLIEWYDFHVYTTFSIFFAASFFPRE 57 Query: 61 DTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGY 120 + T QLL+TAAIFA+GFL+RP+G WL+GLYADR GR++AL SV LMC GSL I L P Y Sbjct: 58 NRTIQLLSTAAIFAIGFLLRPVGSWLIGLYADRRGRRSALTLSVILMCAGSLAIGLCPTY 117 Query: 121 ETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIA 180 IG+ AP++L+ ARL+QG S+GGEYG S+ YLSE+A RGF+SSF YVTLI GQL+A Sbjct: 118 PQIGMAAPLVLLLARLVQGFSLGGEYGASSVYLSEIARPGHRGFYSSFHYVTLILGQLLA 177 Query: 181 LGVLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESF-AKKEKSKESAM 239 V +VLQ + +L DWGWR+PF GA A+VA ++RR ++ET F A EK K Sbjct: 178 TLVQVVLQALIPRAELIDWGWRVPFITGAALALVAWWVRRNIDETPDFRALDEKDKRGVS 237 Query: 240 RTLLR-HPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMC 298 + LR H + ++ V GLT GGTLAF+TYT YM YLVNTVG+S S +S +TL LFM Sbjct: 238 LSALREHWRPVLLVFGLTTGGTLAFFTYTVYMHNYLVNTVGLSAQTSAWLSLSTLTLFMV 297 Query: 299 LQPIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYT 358 +QP G LSD++GRRP+L+ FGI GT T P+LT L + AF L+ AL+IVSGYT Sbjct: 298 VQPFFGALSDRIGRRPLLLWFGIGGTFGTWPLLTALAHTHSATTAFLLLALALMIVSGYT 357 Query: 359 SINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIA 418 S+ +V+KA+LFP +RALGVG+PYA+ ++FGGTA Y LWFKSIG E+G+Y Y +ACI Sbjct: 358 SVCSVMKAQLFPARLRALGVGVPYAIATAVFGGTASYAGLWFKSIGHESGFYLYASACIG 417 Query: 419 VSLLVYVTMKDT 430 +L+ ++++ + Sbjct: 418 CTLIATLSLRSS 429 Lambda K H 0.325 0.138 0.414 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: 647 Number of extensions: 39 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: 435 Length adjustment: 32 Effective length of query: 407 Effective length of database: 403 Effective search space: 164021 Effective search space used: 164021 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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