Align Alpha-ketoglutarate permease (characterized)
to candidate BWI76_RS21415 BWI76_RS21415 MFS transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Koxy:BWI76_RS21415 Length = 432 Score = 749 bits (1934), Expect = 0.0 Identities = 374/432 (86%), Positives = 397/432 (91%) Query: 1 MAESTVTADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTT 60 M ES+++ DTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTT Sbjct: 1 MTESSISERESQDHGDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTT 60 Query: 61 QLLQTAGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIG 120 QLLQTAGVFAAGFLMRPIGGW+FGRIAD+ GRK SML+SVCMMCFGSLVIACLPGY TIG Sbjct: 61 QLLQTAGVFAAGFLMRPIGGWIFGRIADRRGRKTSMLISVCMMCFGSLVIACLPGYATIG 120 Query: 121 TWAPALLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVV 180 TWAPALLLLARLFQGLSVGGEYGTSATYMSEVAVEG+KGFYASFQYVTLIGGQLLA+LVV Sbjct: 121 TWAPALLLLARLFQGLSVGGEYGTSATYMSEVAVEGKKGFYASFQYVTLIGGQLLAVLVV 180 Query: 181 VVLQHTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWR 240 V LQ + D AL WGWRIPFALGAVLA+VALWLRRQLDETS+QETRALKEAGS KGLWR Sbjct: 181 VALQQILSDEALHAWGWRIPFALGAVLAIVALWLRRQLDETSKQETRALKEAGSFKGLWR 240 Query: 241 NRRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIG 300 NR+AFIMVLGFTAAGSL FYTFTTYMQKYLVNTAGM A AS IMTAALFV+ML+QPL G Sbjct: 241 NRKAFIMVLGFTAAGSLSFYTFTTYMQKYLVNTAGMTAGTASMIMTAALFVYMLVQPLFG 300 Query: 301 ALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGIL 360 ALSDKIGRRTSMLCFG L +FTVPIL+ALQNVSSPYAAF LV+CALLIVSFYTSISGIL Sbjct: 301 ALSDKIGRRTSMLCFGVLVTVFTVPILNALQNVSSPYAAFALVICALLIVSFYTSISGIL 360 Query: 361 KAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSLKSIGMETAFFWYVTLMAVVAFLVS 420 KAEMFPAQVRALGVGLSYAVANA+FGGSAEYVALSLKS G+E AF+WYVT+M +AFLVS Sbjct: 361 KAEMFPAQVRALGVGLSYAVANALFGGSAEYVALSLKSAGIEHAFYWYVTVMGAIAFLVS 420 Query: 421 LMLHRKGKGMRL 432 L LHRKGKG+RL Sbjct: 421 LTLHRKGKGLRL 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: 716 Number of extensions: 14 Number of successful extensions: 3 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: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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