Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate Ac3H11_3022 putative sugar transport protein
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3022 Length = 543 Score = 206 bits (524), Expect = 2e-57 Identities = 128/382 (33%), Positives = 206/382 (53%), Gaps = 18/382 (4%) Query: 15 EYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLM 74 E RK IFA +S G + EW+DFY+Y A A FF D S + FAAGF++ Sbjct: 4 EERKVIFA---SSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDSGSAFIFALLAFAAGFIV 60 Query: 75 RPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQG 134 RP G FGR+ D GRK + L+++L+M + V ++PTYA+IG AP +L++ RL QG Sbjct: 61 RPFGAIFFGRLGDMIGRKYTFLVTILIMGLSTFIVGILPTYASIGVAAPIILIVLRLLQG 120 Query: 135 LSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELMAW 194 L++GGEYG +ATY++E AP+GRRG + ++ T G L+++V+ G + + + W Sbjct: 121 LALGGEYGGAATYVAEHAPHGRRGAYTAWIQTTATLGLFLSLMVILGTRTIVGEEAFADW 180 Query: 195 GWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQH--------KRAFLN 246 GWRVPF++ V +++++R ++ E S A + K + T K L+ K L Sbjct: 181 GWRVPFIVSIVLLAISVWIRLAMNE-SPAFQKMKAEGKTSKAPLKESFGEWKNLKIVILA 239 Query: 247 VVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIG 306 +VG TAG ++++Y+ Y +L +D AN ++ +L + +FG++SDKIG Sbjct: 240 LVGLTAGQAVVWYSGQFYALFFLTQALKVDGATANILVAVSLLIGTPFFIVFGSLSDKIG 299 Query: 307 RRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIV------SFYTSISGLIK 360 R+ +L + FP+ L ++P +A A A + +V SF + +G +K Sbjct: 300 RKPIILAGCLLAALTYFPVFGALTKAANPALAEAQAKNKVVVVADANECSFQFNPTGTVK 359 Query: 361 AEMFPPEVRALGVGLSYAVGNA 382 + + G S + NA Sbjct: 360 FTSSCDIAKQVLAGASVSYENA 381 Score = 36.6 bits (83), Expect = 2e-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: 445 VTAILVYLVLLVTMVYGPIAAML-VEMFPTRIRYTSMSLPYHIGNGWFGGLLPTTAFAIV 503 Query: 396 KSAGIESAFYWYVSALCLVALII 418 G WY + ++I Sbjct: 504 AQTGNMYNGLWYPIIIAAATVVI 526 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: 651 Number of extensions: 36 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 457 Length of database: 543 Length adjustment: 34 Effective length of query: 423 Effective length of database: 509 Effective search space: 215307 Effective search space used: 215307 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 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