Align Alpha-ketoglutarate permease (characterized)
to candidate WP_018126083.1 B149_RS0115480 MFS transporter
Query= SwissProt::P0AEX3 (432 letters) >NCBI__GCF_000375485.1:WP_018126083.1 Length = 422 Score = 224 bits (572), Expect = 3e-63 Identities = 134/415 (32%), Positives = 215/415 (51%), Gaps = 16/415 (3%) Query: 19 RRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPI 78 +R A++ GN+VEW+DF +Y + + + +FFP + T L+ T G+FAAGF MRP+ Sbjct: 5 KRHTALLAGFIGNVVEWYDFALYGYMAGIISTLFFPQQSDTAGLIATYGIFAAGFFMRPL 64 Query: 79 GGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGLSV 138 G + G + D GR ++M++SV MM ++++ CLP Y+TIG WAP LL++ R+ QGLSV Sbjct: 65 GSGILGWMGDTLGRSRTMMISVIMMVLPTVLLGCLPTYDTIGLWAPVLLVIIRMVQGLSV 124 Query: 139 GGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAALREWGWR 198 GGE+ +S TY+ E A + +G S+ + G LL L + + WGWR Sbjct: 125 GGEFSSSVTYLVETASDDGRGLAGSWANTGSMAGMLLGSGAAAALTNLFPSDFVHSWGWR 184 Query: 199 IPFALGAVLAVVALWLRRQLDET--------SQQETRALKEAGSLKGLWRNRRAFIMVLG 250 IPF LG ++ +A+ LRR+L ++ + ET L EA NR+ I + Sbjct: 185 IPFLLGGIIGGLAILLRRRLPQSDHFQNHHEERDETSPLLEA-----FTTNRKQMIQAIL 239 Query: 251 FTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRT 310 F +A + FY Y ++L GM +A I TA + + + P+ G L D++ RRT Sbjct: 240 FASAYGILFYIPLVYFPEWLHRETGMERELALQINTAGTALLLALIPVSGWLGDRLIRRT 299 Query: 311 SMLCFGS-LAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQV 369 ++ L + VP+ L N Y A + ++V+ + + E+FPA Sbjct: 300 RLISMTMFLLMLCAVPLYVWLAN-DGLYGAIAVQFLLAMLVAVPLGSAPAMFVELFPACD 358 Query: 370 RALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVAFLVSLML 423 R G ++Y + + GG+ +A SL + G A + ++AF V+L + Sbjct: 359 RLSGYSVAYNIGLGVVGGATPMLATSLIEMTGSSVAPAALLATAGLMAFAVTLWM 413 Lambda K H 0.328 0.138 0.419 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: 436 Number of extensions: 22 Number of successful extensions: 4 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: 432 Length of database: 422 Length adjustment: 32 Effective length of query: 400 Effective length of database: 390 Effective search space: 156000 Effective search space used: 156000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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