Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate PP_2411 PP_2411 Major facilitator family transporter
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__Putida:PP_2411 Length = 445 Score = 244 bits (624), Expect = 3e-69 Identities = 145/411 (35%), Positives = 216/411 (52%), Gaps = 7/411 (1%) Query: 23 ILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLMRPIGGWLF 82 I ++ GN VEWFDF VY F A A FF D + LL T VFA F +RP+GG +F Sbjct: 16 IAASAIGNFVEWFDFAVYGFLATLIASQFFASEDASVALLKTFAVFAVAFALRPLGGIVF 75 Query: 83 GRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQGLSVGGEYG 142 G + D+ GRK + +++L+M G + + ++PTYA+IG APALL LAR QG S GGEY Sbjct: 76 GALGDRLGRKRILSLTILLMAGSTTLIGLLPTYASIGLAAPALLTLARCLQGFSAGGEYA 135 Query: 143 TSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELMAWGWRVPFVL 202 + Y+ E AP+ +R F+ SF V+ A ++ +G++ L+ + AWGWR+PF++ Sbjct: 136 GACAYLMEHAPDDKRAFYGSFVPVSTFSAFACAAVIAYGLEASLSTEAMNAWGWRIPFLI 195 Query: 203 GAVGALVAMYLRSSLAET----SSAGARKKKDAGTLKGLLQHK-RAFLNVVGFTAGGSLM 257 A LV +YLR + ET + K+ + LK L+H R N+ F + +L Sbjct: 196 AAPLGLVGLYLRWRMEETPAFREAVAQGKEHEHSPLKETLRHHGRVIRNLGAFISLTALS 255 Query: 258 FYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGRRNSMLCFAFF 317 FY FTTY YL + + V T AL + P+ GA SD++GRR ++ + Sbjct: 256 FYMFTTYFATYLQLVGNLTRAQSLLVTTVALLFAAVGCPLAGAFSDRVGRRKTIGFTCLW 315 Query: 318 GMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEMFPPEVRALGVGLSY 377 M+ FP S G + + +LA+ + + L+ +E FP R ++Y Sbjct: 316 VMLCVFPAYWLASSGSMSGALLGVILLAVGALCSGVVTAALL-SESFPTRTRYTASAITY 374 Query: 378 AVGNAIFGGSAEFVALSL-KSAGIESAFYWYVSALCLVALIISLRMPDPQR 427 V +FGG+A VA L G A +Y+ + LVAL+ L +P+ R Sbjct: 375 NVAYTLFGGTAPLVATWLIAQTGSSLAPAFYLVVIALVALVGGLALPETSR 425 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: 577 Number of extensions: 32 Number of successful extensions: 6 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: 445 Length adjustment: 33 Effective length of query: 424 Effective length of database: 412 Effective search space: 174688 Effective search space used: 174688 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