Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate 16092 b1981 shikimate transporter (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__Keio:16092 Length = 438 Score = 219 bits (557), Expect = 2e-61 Identities = 138/428 (32%), Positives = 208/428 (48%), Gaps = 10/428 (2%) Query: 15 PARERTTASRIKSIFSGS-VGNMVEWYDWYVYA-AFSLYFAKVFFPKGDTTAQLLNTAAI 72 P + SR + GS G +V+WYD+ +Y +L F + FFP+ L A Sbjct: 10 PDEGTLSLSRARRAALGSFAGAVVDWYDFLLYGITAALVFNREFFPQVSPAMGTLAAFAT 69 Query: 73 FAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLV 132 F VGFL RP+GG + G + DR GRKR LM +V++M + +I + PS+ TIG APILLV Sbjct: 70 FGVGFLFRPLGGVIFGHFGDRLGRKRMLMLTVWMMGIATALIGILPSFSTIGWWAPILLV 129 Query: 133 FARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLT 192 R +QG +VGGE+G +A E A K ++ F+SS V G L++ G++ ++ T Sbjct: 130 TLRAIQGFAVGGEWGGAALLSVESAPKNKKAFYSSGVQVGYGVGLLLSTGLVSLISMMTT 189 Query: 193 TEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKE------KSKESAMRTLLRHP 246 EQ +WGWRIPF + + AL++R GMEE+ F +++ K + + LLRHP Sbjct: 190 DEQFLSWGWRIPFLFSIVLVLGALWVRNGMEESAEFEQQQHYQAAAKKRIPVIEALLRHP 249 Query: 247 KELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGL 306 + ++ L + L Y T + Y +G+ I L P L Sbjct: 250 GAFLKIIALRLCELLTMYIVTAFALNYSTQNMGLPRELFLNIGLLVGGLSCLTIPCFAWL 309 Query: 307 SDKIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKA 366 +D+ GRR + I ++GTL P L +W FF IM A I + + Sbjct: 310 ADRFGRRRVYITGTLIGTLSAFPFFMALEAQSIFWIVFFSIMLANIAHDMVVCVQQPMFT 369 Query: 367 ELFPTEIRALGVGLPYALTVSIFGGTAEYI--ALWFKSIGMETGYYWYVTACIAVSLLVY 424 E+F R G G+ Y + + GG +I AL G Y+ A +S + Sbjct: 370 EMFGASYRYSGAGVGYQVASVVGGGFTPFIAAALITYFAGNWHSVAIYLLAGCLISAMTA 429 Query: 425 ITMKDTRK 432 + MKD+++ Sbjct: 430 LLMKDSQR 437 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: 567 Number of extensions: 33 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: 439 Length of database: 438 Length adjustment: 32 Effective length of query: 407 Effective length of database: 406 Effective search space: 165242 Effective search space used: 165242 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 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