Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_011799906.1 PNAP_RS02410 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000015505.1:WP_011799906.1 Length = 552 Score = 205 bits (522), Expect = 3e-57 Identities = 121/346 (34%), Positives = 189/346 (54%), Gaps = 12/346 (3%) Query: 5 TQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNT 64 T + AE RK IFA +S G + EW+DFY+Y A A FF D S + Sbjct: 3 TTVDKSVMTAEQRKVIFA---SSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDAGSAFIFA 59 Query: 65 AGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPA 124 FAAGF++RP G +FGR+ D GRK + L+++++M + V ++P+YA+IG AP Sbjct: 60 LLAFAAGFIVRPFGALVFGRLGDMIGRKYTFLVTIVIMGLSTFIVGLLPSYASIGVAAPV 119 Query: 125 LLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQ 184 +L+ R+ QGL++GGEYG +A Y++E AP GRRG + S+ T G L++LV+ G++ Sbjct: 120 ILIALRMLQGLALGGEYGGAAVYVAEHAPEGRRGAYTSWIQTTATMGLFLSLLVILGVRT 179 Query: 185 WLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQH---- 240 + + WGWRVPFV+ + V++Y+R S+ E S A + K + T K L Sbjct: 180 AVGEVAFADWGWRVPFVVSILLLAVSVYIRLSMNE-SPAFQKMKAEGRTSKAPLSESFGQ 238 Query: 241 ----KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQP 296 K L +VG TAG ++++Y+ Y +L +D AN ++ +L + Sbjct: 239 WKNLKIVILALVGLTAGQAVVWYSGQFYSLFFLTQALKVDGPTANILVAYSLLLATPFFV 298 Query: 297 IFGAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALA 342 +FG +SDKIGR+ ++ + FP+ L ++P +A A A Sbjct: 299 VFGTLSDKIGRKPIIMAGCLLAALTYFPVFTALTKAANPDLAEAQA 344 Score = 35.4 bits (80), Expect = 5e-06 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 2/83 (2%) Query: 337 VAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSL- 395 V L L L + Y I+ ++ EMFP +R + L Y +GN FGG A ++ Sbjct: 454 VTAILFYLVLLVTMVYGPIAAML-VEMFPTRIRYTSMSLPYHIGNGWFGGLLPTTAFAIV 512 Query: 396 KSAGIESAFYWYVSALCLVALII 418 G WY + V ++ Sbjct: 513 AQTGNMYNGLWYPIIIAGVTFVV 535 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: 627 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 457 Length of database: 552 Length adjustment: 34 Effective length of query: 423 Effective length of database: 518 Effective search space: 219114 Effective search space used: 219114 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: 52 (24.6 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