Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate GFF1423 PS417_07230 citrate-proton symporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__WCS417:GFF1423 Length = 435 Score = 239 bits (611), Expect = 1e-67 Identities = 142/431 (32%), Positives = 226/431 (52%), Gaps = 22/431 (5%) Query: 15 PAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFA 74 P + + S++ ++F + GN +E +D++++ ++ Y A AFFP + A L+ T A+F Sbjct: 4 PTRPDSARSKVGAVFRVTSGNFLEQFDFFLFGFYATYIAAAFFPAANEFASLMMTFAVFG 63 Query: 75 VGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFA 134 GFLMRP+G ++G Y D GR+ L+ ++ +M G+L+I L P Y TIG+ AP+L++ Sbjct: 64 AGFLMRPLGAIILGAYIDDVGRRKGLIVTLSIMASGTLLIVLVPSYHTIGLWAPLLVLLG 123 Query: 135 RLLQGLSVGGEYGTSATYLSEMATKERRGFFSSF----QYVTLISGQLIALGVLIVLQQT 190 RLLQG S G E G + YLSEMAT R+GF++S+ Q ++++ + G+ + ++ Sbjct: 124 RLLQGFSAGAELGGVSVYLSEMATPGRKGFYTSWQSGSQQISIVVAAALGYGLNVWMEPA 183 Query: 191 LTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKELM 250 + DWGWRIPFAIG + LRR ++ETE FA + K + + L K Sbjct: 184 VVA----DWGWRIPFAIGCVIIPFIFILRRSLQETEEFANR-KHRPTMREVLATLVKNWT 238 Query: 251 TVVG---LTMGGTLAFYTYTTYMQKYLVNTVGMSISDS---TTISAATLFLFMCLQPIIG 304 V+G + T AFY T Y + + +S SD+ T + A + F+++ PI G Sbjct: 239 VVIGGMLMVAMTTTAFYLITVYAPTFGKTVLQLSTSDALLVTLLVAVSNFIWL---PIGG 295 Query: 305 GLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVV 364 LSD+ GR+P+LIA +L L P L+ + ++ ++ + Y Sbjct: 296 TLSDRFGRKPVLIAMTVLTVLTAYPALSYVVNAPSFAHMLETLLWFSFLYGLYNGAMIPA 355 Query: 365 KAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGME--TGYYW--YVTACIAVS 420 E+ P E+R G L Y+L +IFGG I+ WF I + + YW + AC S Sbjct: 356 LTEIMPVEVRVAGFSLAYSLATAIFGGFTPAISTWFIHITEDKASPAYWMMFAAACALCS 415 Query: 421 LLVYVTMKDTR 431 L + R Sbjct: 416 TLALYRRANAR 426 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: 541 Number of extensions: 34 Number of successful extensions: 6 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: 435 Length adjustment: 32 Effective length of query: 407 Effective length of database: 403 Effective search space: 164021 Effective search space used: 164021 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