Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate Pf1N1B4_5606 Alpha-ketoglutarate permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5606 Length = 461 Score = 492 bits (1266), Expect = e-143 Identities = 242/431 (56%), Positives = 316/431 (73%), Gaps = 3/431 (0%) Query: 3 DTTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLL 62 D + P+ A R+ AI+GA SGNLVEW+DF++Y++ AIYFA +FFPKGD TSQLL Sbjct: 13 DHAAETAPMKAPN---RVKAIMGACSGNLVEWYDFFIYAYTAIYFAASFFPKGDTTSQLL 69 Query: 63 NTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWA 122 TAGVFA GF MRP+GGW+FG IAD GRK SM+ISV MMC GSL +AVMPTYATIG A Sbjct: 70 ATAGVFAVGFFMRPLGGWIFGWIADTRGRKVSMIISVFMMCAGSLLIAVMPTYATIGVAA 129 Query: 123 PALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGM 182 P LL++ARL QGLSVG EYGT ATY+SE+A GRR F+ SFQY T+I GQLLA++ + + Sbjct: 130 PILLVVARLIQGLSVGAEYGTGATYISEIATPGRRCFYGSFQYFTIIAGQLLALMTVVIL 189 Query: 183 QQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQHKR 242 QQ LT EL WGWR+PF +GA+ ++V +YLR ++ ET++ +KDAG+L+G+ +HKR Sbjct: 190 QQTLTGEELREWGWRIPFFIGALSSIVVVYLRRAMHETATKKDMNRKDAGSLRGMFKHKR 249 Query: 243 AFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAIS 302 A VV FT GGSL FYTFTTYMQK+LV +AG P+ + +MT AL +M QP+FG ++ Sbjct: 250 AVALVVAFTIGGSLYFYTFTTYMQKFLVISAGFSPETVSFIMTAALVGFMFCQPLFGLLA 309 Query: 303 DKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAE 362 D+IG + ML F+ M+ P+L+ L+ VSSP A L L I S YT I+G++KAE Sbjct: 310 DRIGIKAHMLMFSGLAMLLVIPLLYSLQSVSSPFTAFLLVFGGLAIASLYTPIAGIVKAE 369 Query: 363 MFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISLRM 422 +FPP VRALGVG YAVGNA FGG+AE+VALSL+S G+E+ F++YV+A+ + I ++ M Sbjct: 370 LFPPAVRALGVGFPYAVGNAAFGGTAEYVALSLRSQGVEAYFFFYVAAVVTITFIAAMLM 429 Query: 423 PDPQRDGHLKG 433 P+ R G++ G Sbjct: 430 PNLSRYGYISG 440 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: 653 Number of extensions: 30 Number of successful extensions: 3 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: 461 Length adjustment: 33 Effective length of query: 424 Effective length of database: 428 Effective search space: 181472 Effective search space used: 181472 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