Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_013459347.1 SULKU_RS02455 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000183725.1:WP_013459347.1 Length = 409 Score = 172 bits (435), Expect = 2e-47 Identities = 110/361 (30%), Positives = 173/361 (47%), Gaps = 12/361 (3%) Query: 29 GNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLMRPIGGWLFGRIADK 88 GN++E++DF + F A+ FFP DP LL + G FAAG +MRP+G +FG I D+ Sbjct: 14 GNVIEYYDFALIGFLAVMMGNLFFPSHDPFLSLLGSFGAFAAGMIMRPVGALIFGHIGDR 73 Query: 89 HGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQGLSVGGEYGTSATYM 148 R+T+++ S+LMM + + +PTYA IG AP LL+L R+ QGLSVGGEY +S Y+ Sbjct: 74 VSRRTALMSSLLMMALPTFLIGFLPTYAQIGILAPILLVLLRMIQGLSVGGEYASSIVYL 133 Query: 149 SEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELMA-WGWRVPFVLGAVGA 207 E + + + SF V G L G W + M WGWR+PF + A Sbjct: 134 VEQSAPDHQNLYGSFVSVGAKIGMALG-SGFCGALLWYIGGDAMGEWGWRIPFWASIIIA 192 Query: 208 LVAMYLRSSLAETSSAGARKKKDAGTLKGLLQHKRAFLNVVGFTAGGSLMFYTFTTYMQK 267 +YLR +L T + K + L H+R F + + + +YT Y+ Sbjct: 193 AAGLYLRRNL--TDDYRPSEDKTVPIVAILRHHRREFWQFLTIASAIWVFYYTVFIYLPI 250 Query: 268 YLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGRRNSMLCFAFFGMVGTFPILH 327 +L +AG+ A + T ++ V ++ P+ ++D IG M + + +P+ + Sbjct: 251 WLEGSAGLSKAEAGQINTLSIVVGVVFIPLMAMVADVIGSLRLMRLTSITLAISVYPLFY 310 Query: 328 FLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGS 387 ++ G L + + +F +A +F V AL A A+ GS Sbjct: 311 WMSIGGFWGALAGTIGLVILLCAF--------QAPIFASTVNALHYHGYRASFTAVILGS 362 Query: 388 A 388 A Sbjct: 363 A 363 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: 584 Number of extensions: 37 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: 409 Length adjustment: 32 Effective length of query: 425 Effective length of database: 377 Effective search space: 160225 Effective search space used: 160225 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