Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate WP_012384331.1 BIND_RS06770 MFS transporter
Query= uniprot:D8J257 (457 letters) >NCBI__GCF_000019845.1:WP_012384331.1 Length = 568 Score = 201 bits (512), Expect = 4e-56 Identities = 127/350 (36%), Positives = 196/350 (56%), Gaps = 15/350 (4%) Query: 10 PLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTAGVFA 69 P+S+AE RK IFA +S G + EW+DFY+Y A FF + T+ + FA Sbjct: 16 PMSSAE-RKVIFA---SSLGTVFEWYDFYLYGSLASIIGAQFFSQFPKTTADIFALLAFA 71 Query: 70 AGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPALLLLA 129 AGFL+RP G +FGR+ D GRK + L+++L+M + V ++P Y +IG AP +L+ A Sbjct: 72 AGFLVRPFGALVFGRLGDLVGRKYTFLVTILIMGLSTFVVGLLPNYDSIGIAAPIILISA 131 Query: 130 RLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQWLTKA 189 RL QGL++GGEYG +ATY++E AP+GRRGF+ S+ T G L++LV+ G + + +A Sbjct: 132 RLLQGLALGGEYGGAATYVAEHAPHGRRGFYTSWIQTTATLGLFLSLLVILGTRTFFGEA 191 Query: 190 ELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTL--KGLLQ-------H 240 GWRVPF++ + LV++++R L+E S K K+ GT+ K L + Sbjct: 192 RFAEIGWRVPFIVSVLLLLVSLWIRLQLSE--SPAFLKMKEEGTVSEKPLTEAFATWSNA 249 Query: 241 KRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFGA 300 K A L + G T G +++YT Y +L + +D AN ++ AL FG Sbjct: 250 KIALLALFGLTMGQGVVWYTGQFYSLFFLQSICKVDGYTANLLIAWALVCGTGFFVFFGW 309 Query: 301 ISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVS 350 +SD IGR+ +L + FPI + ++P +A AL + + +V+ Sbjct: 310 LSDHIGRKPIILTGCLLAALTYFPIYRAITANANPALAQALETVKVKVVA 359 Score = 40.4 bits (93), Expect = 2e-07 Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 8/100 (8%) Query: 331 DVSSPGVAMALAILALTIVSFYTSISGLIKA---EMFPPEVRALGVGLSYAVGNAIFGGS 387 D+S P V + +LA+ ++ + T + G I A E+FP +R + L Y +GN FGG Sbjct: 461 DLSEPRVLHLIGLLAILVI-YVTMVYGPIAAALVELFPTRIRYTSMSLPYHIGNGWFGGL 519 Query: 388 AEFVALSLKSAGIESAFY--WYVSALCLVALII-SLRMPD 424 A ++ A +Y WY + +I SL +P+ Sbjct: 520 LPATAFAM-VAQTGDIYYGLWYPIIFAGITFVIGSLFIPE 558 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: 697 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 457 Length of database: 568 Length adjustment: 34 Effective length of query: 423 Effective length of database: 534 Effective search space: 225882 Effective search space used: 225882 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 24 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