Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_052306240.1 BPHY_RS31270 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000020045.1:WP_052306240.1 Length = 438 Score = 233 bits (595), Expect = 7e-66 Identities = 145/426 (34%), Positives = 225/426 (52%), Gaps = 13/426 (3%) Query: 1 MSDTTQASTPLSAAEYRKRIFAILGASS-GNLVEWFDFYVYSFCAIYFAPAFFPKGDPTS 59 M D+T + +AA K + AS GN VEWFD+ Y + A A FFPK D ++ Sbjct: 1 MRDSTSGDSSANAAVDPKLLRRAAFASFIGNFVEWFDYASYGYLATIIAVVFFPKTDGSA 60 Query: 60 QLLNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIG 119 LL GVFA F++RP+GG ++G DK GR+ S+ +S+L+M + +A++PTYA +G Sbjct: 61 GLLAAYGVFAISFIVRPVGGIVWGHFGDKIGRRASLSLSILIMSASTFVIALLPTYAQVG 120 Query: 120 AWAPALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVL 179 AP LLLL R+ QG S GEY ++ +++E AP+ RRGF+ S + G L +++ Sbjct: 121 VLAPVLLLLVRVVQGFSASGEYAGASAFLAEYAPSNRRGFYTSIVPASTAAGLLFGSILI 180 Query: 180 FGMQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKD----AGTLK 235 M L+ +L ++GWR+PF+L A L+ Y+R L +T A +++ A + Sbjct: 181 AIMHAVLSSEQLHSFGWRLPFLLAAPFGLIGRYIRVKLEDTPRFKALEQQSHVARAPIAE 240 Query: 236 GLLQHKRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQ 295 L +H+ L G T ++ FY +YM YL GMD + T +L Y+ L Sbjct: 241 LLGKHRGKMLIAFGVTCLNAVAFYLVLSYMPTYLSTELGMDETASFIAATISLTAYIGLI 300 Query: 296 PIFGAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSI 355 + GA+SD++GR++ ++ + V T P+ K + G M + + + + T Sbjct: 301 FVMGALSDRLGRKSMLIGASILFAVLTVPL---FKGLGGAGF-MTIVAIQIAFGALLTMN 356 Query: 356 SGLIK---AEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSA-GIESAFYWYVSAL 411 G + +E+FP VR G + NA+FGG+A VA L A G + A WY+ Sbjct: 357 DGTLPCFLSEIFPTRVRYSGFAFCFNAANALFGGTAPLVATWLIGATGSKLAPAWYLVGA 416 Query: 412 CLVALI 417 +VALI Sbjct: 417 AIVALI 422 Lambda K H 0.325 0.138 0.418 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: 576 Number of extensions: 32 Number of successful extensions: 4 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: 457 Length of database: 438 Length adjustment: 33 Effective length of query: 424 Effective length of database: 405 Effective search space: 171720 Effective search space used: 171720 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 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