Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate AO353_05775 AO353_05775 MFS transporter
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05775 Length = 446 Score = 238 bits (606), Expect = 4e-67 Identities = 150/420 (35%), Positives = 229/420 (54%), Gaps = 19/420 (4%) Query: 17 RKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFAAGFLMRP 76 R+R A +GA+SG+L+EW+D+ VY F A+Y AFF DPTS LL + FA F +RP Sbjct: 10 RQRRRAFIGATSGHLIEWYDYGVYGFLAVYIGKAFFVSDDPTSSLLASFAAFALSFFIRP 69 Query: 77 IGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLARLFQGLS 136 +GG FG +ADK GR+ +++ ++MM G ++ + ++PTYAT+G AP LL+L R QG S Sbjct: 70 LGGLFFGPLADKIGRRKTLITVLVMMAGSTVLLGLLPTYATLGIAAPILLVLIRCVQGFS 129 Query: 137 VGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKAELM-AWG 195 GGE GT +++SE A GRRGF + VT + G LL V GM W+ A+LM AWG Sbjct: 130 AGGEIGTITSFISEYAGPGRRGFATCWLMVTAVLGLLLGGAVANGMT-WVMGADLMQAWG 188 Query: 196 WRVPFVLGAVGALVAMYLRSSLAETSSAGARKK---KDAGTLKGLLQHKRAFLNVVGFTA 252 WR+PF++ A L++MY+R L ++ A ++ L+ + Q KRA V Sbjct: 189 WRIPFLIAAPLGLISMYIRLKLEDSPEFLALQRAGETSKAPLREVWQWKRAIALVFFIIT 248 Query: 253 GGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGAISDKIGRRNSML 312 S +FY T+ Y+ + D + A ++ P GA +DK GR+ +L Sbjct: 249 LHSSIFYLVLTFASTYMSSILKFDSGTTLLYVFVASLSAAVVMPFGGAFTDKYGRKPFLL 308 Query: 313 CFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS----FYTSISGLIKAEMFPPEV 368 G + T + K S+P A I L V+ Y S + + +E+ P + Sbjct: 309 ---VVGTLATLAMYWLFK--SAPTATPASFIYPLMTVAILFGLYASSTYALMSELLPTRI 363 Query: 369 RALGVGLSYAVGNAIFGGSAEFVA--LSLKSAGIESAFYWYV--SALCLVALIISLRMPD 424 R+ G+ ++Y + A+FGGSA ++ L + I S +Y+Y+ + L+AL++ LR D Sbjct: 364 RSTGIAVAYNIPVAVFGGSAPLISTWLIKVTGDITSPWYFYIGTGVVSLIALVL-LRKED 422 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: 605 Number of extensions: 38 Number of successful extensions: 5 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: 446 Length adjustment: 33 Effective length of query: 424 Effective length of database: 413 Effective search space: 175112 Effective search space used: 175112 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