Align Alpha-ketoglutarate permease (characterized)
to candidate BPHYT_RS03430 BPHYT_RS03430 major facilitator transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__BFirm:BPHYT_RS03430 Length = 425 Score = 247 bits (631), Expect = 4e-70 Identities = 148/432 (34%), Positives = 230/432 (53%), Gaps = 13/432 (3%) Query: 6 VTADSKLTSSDTRRRIW-AIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQ 64 + A + + + +R+ W A++ AS GN +EWFD VY F ++ A +FFP+GN T LL Sbjct: 1 MNATTAASLAGSRQNSWRAVIAASIGNALEWFDLVVYGFFAVIIAKLFFPAGNDTVSLLL 60 Query: 65 TAGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAP 124 T G F F MRP+G + G AD+ GRK ++ LS+ +M G+L+IA LP Y++IG AP Sbjct: 61 TLGTFGVSFFMRPLGAIVIGAYADRAGRKAALTLSILLMMGGTLIIAILPTYQSIGLAAP 120 Query: 125 ALLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQ 184 +L+LARL QG S GGE+G++ +++E V GR+GF+AS+Q + LLA V+L Sbjct: 121 VILVLARLMQGFSAGGEFGSATAFLAE-HVPGRRGFFASWQVASQGLTTLLAAGFGVLLT 179 Query: 185 HTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWRNRRA 244 + + WGWR+PF G ++ VA ++R +LDET + E + Sbjct: 180 GKLSPEQMASWGWRVPFFFGLLIGPVAWYIRTKLDETPEFLAAETTETPLRDTFTSQKLR 239 Query: 245 FIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSD 304 ++ +G G++ Y +M + V G+ +VA + + M+ PL+G LSD Sbjct: 240 LLIAIGVVVLGTVSTY-LVLFMPTFGVKQLGLAPSVAFSAIALTGLIQMVFSPLVGHLSD 298 Query: 305 KIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGL-----VMCALLIVSFYTSISGI 359 + GR T ML L + P L V+ P FG ++ L+ ++ ++ G+ Sbjct: 299 RHGRTTIMLSSALLLLVLIYPAFVYL--VAHP--TFGTLIAMQIVFGFLMTGYFAALPGL 354 Query: 360 LKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSLKSIGMETAFFWYVTLMAVVAFLV 419 L +EMFP Q R G+ L+Y +A IFGG ++ L S+ A Y + A + LV Sbjct: 355 L-SEMFPVQTRTTGMSLAYNIAVTIFGGFGPFIIAWLISVTGSKAAPSYYLIFAAIVSLV 413 Query: 420 SLMLHRKGKGMR 431 +L R+ G R Sbjct: 414 ALTAARRKLGFR 425 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: 478 Number of extensions: 25 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: 432 Length of database: 425 Length adjustment: 32 Effective length of query: 400 Effective length of database: 393 Effective search space: 157200 Effective search space used: 157200 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 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