Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate H281DRAFT_04917 H281DRAFT_04917 MFS transporter, MHS family, proline/betaine transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Burk376:H281DRAFT_04917 Length = 433 Score = 254 bits (650), Expect = 3e-72 Identities = 148/434 (34%), Positives = 230/434 (52%), Gaps = 17/434 (3%) Query: 11 SAAVPAKEKTTA-SRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNT 69 S+ VP T A R +I + +GN +EW+D+ VY+ F++ AK FFP G+ LL Sbjct: 6 SSNVPLSVDTLARQRRHAIIATVLGNGLEWFDFTVYSFFAVIIAKLFFPTGNDLTSLLLA 65 Query: 70 AAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPI 129 A F VGF MRP+GG ++G+YAD+ GRKAAL ++ LM G+ +I ++P Y+ IG+ AP+ Sbjct: 66 VATFGVGFFMRPVGGIVLGVYADKVGRKAALSLTILLMAGGTALIGIAPTYQQIGLWAPV 125 Query: 130 LLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ 189 L+V ARLLQG S GGE G++ +L+E A +R ++SS+ ++ L+ V + Sbjct: 126 LIVIARLLQGFSAGGEMGSATAFLTEYAPANKRAYYSSWIQSSIGFAVLLGAAVGTFVTS 185 Query: 190 TLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESF---AKKEKSKESAMRTLLRHP 246 +L+TE L+ WGWR+PF IG L V ++R M+ET +F A + K R P Sbjct: 186 SLSTEALHSWGWRMPFLIGMLIGPVGYFIRSRMDETPAFSAVADEAKDDSPLAEVFRRFP 245 Query: 247 KELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGL 306 +E + + T+ Y YM Y V T+ + S + MC P++G L Sbjct: 246 RETFASFSMVILWTVCTYVLLFYMPTYSVRTLHLPQSTGFLAGMFGGSMIMCFAPVVGKL 305 Query: 307 SDKVGRRPILIAFGILGTLFTVPILTTLH------TIQTWWGAFFLIMAALIIVSGYTSI 360 +D+ GRR L +L + P+ ++ ++ + G F L++AA YT Sbjct: 306 ADRYGRRRFLSGAAVLILVLAWPMFAYINRAPGLASLMVFQGVFGLLIAA------YTGP 359 Query: 361 NAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAV 419 +ELFPT++ + G+ + Y V+IFGG A + W S G +YV A+ Sbjct: 360 ILAAFSELFPTKVLSTGLSVAYNFAVTIFGGFAPFFITWLIASTGSNMAPAFYVMIAAAI 419 Query: 420 SLLVYVTMKDTRKH 433 SL ++D ++H Sbjct: 420 SLTGTFFVRDPQRH 433 Lambda K H 0.325 0.138 0.414 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: 544 Number of extensions: 30 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: 439 Length of database: 433 Length adjustment: 32 Effective length of query: 407 Effective length of database: 401 Effective search space: 163207 Effective search space used: 163207 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