Align Alpha-ketoglutarate permease (characterized)
to candidate WP_057507085.1 ABB28_RS02395 MFS transporter
Query= SwissProt::P0AEX3 (432 letters) >NCBI__GCF_001431535.1:WP_057507085.1 Length = 549 Score = 188 bits (477), Expect = 4e-52 Identities = 109/340 (32%), Positives = 185/340 (54%), Gaps = 12/340 (3%) Query: 4 STVTADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLL 63 ST A ++LT + I +S G + EW+DF++Y + A FF N TT ++ Sbjct: 2 STTPAPAQLTKGHKK----VIFASSLGTVFEWYDFFLYGSLAAIIAKQFFSGVNETTGMI 57 Query: 64 QTAGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWA 123 FAAGF +RP G FG + D+ GRK + L+++ +M + ++ LP Y +IG A Sbjct: 58 FALLAFAAGFFVRPFGAAFFGSLGDRIGRKYTFLVTILIMGISTFLVGVLPNYASIGFAA 117 Query: 124 PALLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVL 183 P +L++ RL QGL++GGEYG +ATY++E A ++G Y SF T G ++LL+++ Sbjct: 118 PVILIILRLAQGLAMGGEYGGAATYVAEHAPANKRGLYTSFIQCTATLGLFMSLLIILAC 177 Query: 184 QHTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWRN-- 241 ++ + + A WGWRIPF + VL +++W+R QL E+ + + GS K +R+ Sbjct: 178 RYFLGNEAFEAWGWRIPFLVSIVLLGISVWIRLQLSESPLFQQMKAEGKGS-KTPFRDSL 236 Query: 242 -----RRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQ 296 + +++LG A ++ +Y Y +L + + A + ++ AAL + + Sbjct: 237 KDGNLKLMLLVLLGAAAGQAVVWYGGQFYALFFLSSMLKVDATTSYLLIAAALALGVPFF 296 Query: 297 PLIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSP 336 G LSD+IGR+ +L LAA+ +P+ L + ++P Sbjct: 297 IFFGWLSDRIGRKWIILAGCLLAAVTYIPVFKGLTHFANP 336 Score = 37.4 bits (85), Expect = 1e-06 Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 5/95 (5%) Query: 333 VSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYV 392 ++ P F L + L + Y I+ L E+FP ++R + L Y + N FGG + Sbjct: 448 INIPGTIFMLWILVLYVTMVYGPIAAYL-VELFPTRIRYTSMSLPYHIGNGWFGGFLPAI 506 Query: 393 ALSLKSIGMETAFF--WYVTLMAVVAFLV-SLMLH 424 + +L + G ++ WY +A++ ++ L LH Sbjct: 507 SFALVA-GTGNLYYGLWYPIAIALMTVVIGGLFLH 540 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: 613 Number of extensions: 37 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: 432 Length of database: 549 Length adjustment: 34 Effective length of query: 398 Effective length of database: 515 Effective search space: 204970 Effective search space used: 204970 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: 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