Align Alpha-ketoglutarate permease (characterized)
to candidate Ga0059261_3322 Ga0059261_3322 Arabinose efflux permease
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Korea:Ga0059261_3322 Length = 445 Score = 463 bits (1192), Expect = e-135 Identities = 228/405 (56%), Positives = 301/405 (74%), Gaps = 1/405 (0%) Query: 16 DTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLM 75 D R R A V S GNL+EW+DFY Y++ +LYFA FFP+G+ T QLL A ++AAGFL+ Sbjct: 29 DRRTRARAAVAGSVGNLIEWYDFYAYAYTALYFASAFFPAGDRTAQLLNVAAIYAAGFLI 88 Query: 76 RPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQG 135 RP+GGW FGR AD+HGR+ +M+ SV +M GSL++ LP Y TIG APALLL+ARL QG Sbjct: 89 RPLGGWFFGRYADRHGRRAAMIASVVLMGAGSLLVGVLPTYATIGAAAPALLLVARLMQG 148 Query: 136 LSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAALREW 195 S GG+YG +ATY+SE+A G++GFYASFQ+VTLIGGQL ALLVV LQ TM + A+REW Sbjct: 149 FSTGGQYGAAATYLSEIAEPGKRGFYASFQFVTLIGGQLFALLVVFALQSTMSETAIREW 208 Query: 196 GWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWRNRRAFIMVLGFTAAG 255 GWR+PF LGAVLA V + R + ET++ ++ ++AGSLK L+++ RA +V+ +AAG Sbjct: 209 GWRLPFLLGAVLAGVFILFRDVMHETAEPASKG-EDAGSLKALFQHPRAMFVVMALSAAG 267 Query: 256 SLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRTSMLCF 315 ++ YTFTTYMQKYLVNTAGM AS M F F+L+QP++G LSD+IGRRT++L F Sbjct: 268 AVTLYTFTTYMQKYLVNTAGMDVASASRTMLIVTFAFLLLQPVLGTLSDRIGRRTNLLIF 327 Query: 316 GSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQVRALGVG 375 +F VP+L A+ + ++A LV AL I+SFYTS+SG+ KAE+FPA+VRALGVG Sbjct: 328 SGGMTLFAVPLLGAIGQAQTMWSAGLLVFAALAIMSFYTSVSGLFKAELFPARVRALGVG 387 Query: 376 LSYAVANAIFGGSAEYVALSLKSIGMETAFFWYVTLMAVVAFLVS 420 L +A+A+AIFGG+AE+ AL LK +G E F WYV+ + VAF+V+ Sbjct: 388 LGHAIASAIFGGTAEWAALMLKQMGHEGLFAWYVSAVCAVAFVVA 432 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: 584 Number of extensions: 28 Number of successful extensions: 2 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: 445 Length adjustment: 32 Effective length of query: 400 Effective length of database: 413 Effective search space: 165200 Effective search space used: 165200 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