Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate PP_1378 PP_1378 alpha-ketoglutarate permease
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__Putida:PP_1378 Length = 429 Score = 599 bits (1544), Expect = e-176 Identities = 299/417 (71%), Positives = 351/417 (84%), Gaps = 1/417 (0%) Query: 8 STPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGV 67 ST + E KRIFAI+GASSGNLVEWFDFYVY+FCAIYFAPAFFP DPT QLLNTAGV Sbjct: 3 STYYTGEERSKRIFAIVGASSGNLVEWFDFYVYAFCAIYFAPAFFPSDDPTVQLLNTAGV 62 Query: 68 FAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLL 127 FAAGFLMRPIGGW+FGR+AD+HGRK S++ISVLMMC GSL +A +PTYA+IG WAPALLL Sbjct: 63 FAAGFLMRPIGGWIFGRLADRHGRKNSLMISVLMMCFGSLMIACLPTYASIGTWAPALLL 122 Query: 128 LARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLT 187 LARL QGLSVGGEYGT+ATYMSEVA G+RGFFASFQYVTLIGGQLLAVLV+ +QQ LT Sbjct: 123 LARLIQGLSVGGEYGTTATYMSEVALRGQRGFFASFQYVTLIGGQLLAVLVVVILQQLLT 182 Query: 188 KAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQ-HKRAFLN 246 + EL AWGWR+PFV+GA+ AL+++ LR SL ETSSA AR KDAG++ GL + H AF+ Sbjct: 183 EDELRAWGWRIPFVVGAIAALISLMLRRSLHETSSAEARNDKDAGSIGGLFRNHAAAFIT 242 Query: 247 VVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIG 306 V+G+TAGGSL+FYTFTTYMQKYLVNTAGM K A+ VMTGALF++M++QP FG +SD+IG Sbjct: 243 VLGYTAGGSLIFYTFTTYMQKYLVNTAGMTAKNASYVMTGALFLFMVVQPFFGMLSDRIG 302 Query: 307 RRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLIKAEMFPP 366 RRNSML F G + T P+L LK V+SP +A L LAL IVSFYTSISGL+KAEMFPP Sbjct: 303 RRNSMLLFGGLGTLCTVPLLMALKTVTSPIMAFVLISLALCIVSFYTSISGLVKAEMFPP 362 Query: 367 EVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIISLRMP 423 +VRALGVGL+YAV NA FGGSAE+VAL LK+ G+E+ FYWYV+A+ +A + SLR+P Sbjct: 363 QVRALGVGLAYAVANAAFGGSAEYVALGLKTLGMENTFYWYVTAMMAIAFLFSLRLP 419 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: 718 Number of extensions: 36 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: 429 Length adjustment: 32 Effective length of query: 425 Effective length of database: 397 Effective search space: 168725 Effective search space used: 168725 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