Align Alpha-ketoglutarate permease (characterized)
to candidate CCNA_00025 CCNA_00025 major facilitator superfamily transporter
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Caulo:CCNA_00025 Length = 550 Score = 169 bits (428), Expect = 2e-46 Identities = 108/336 (32%), Positives = 169/336 (50%), Gaps = 16/336 (4%) Query: 18 RRRIWAIVGASS-GNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMR 76 R + +V ASS G EW+DF+++ + + FF N T + +F GF R Sbjct: 8 RASMRTVVSASSAGTAFEWYDFFIFGSLTQVISKTFFAGLNETAGYIAALALFGVGFAFR 67 Query: 77 PIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGL 136 P+G +FG+I D+ GRK + L +V +M + IA LP YE G AP LL++ R QG Sbjct: 68 PLGALVFGKIGDQDGRKGAFLATVLLMGGATFAIAFLPTYEQAGIIAPILLIILRCLQGF 127 Query: 137 SVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVV----VLQHTMEDAAL 192 ++GGEYG +A Y++E + ++G+ S+ + G ALLV++ VL + A Sbjct: 128 ALGGEYGGAAIYVAEHSPANKRGWATSWVQTSAAFGLFGALLVILATRWVLGKYVGPDAF 187 Query: 193 REWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLK--------GLWRNRRA 244 EWGWRIPFA+ L +++W+R +L E+ E A+K G G W N + Sbjct: 188 DEWGWRIPFAVSLGLLGISVWMRLKLTESPTFE--AMKAEGQASKAPYAEAFGQWSNLKL 245 Query: 245 FIMV-LGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALS 303 I+ + A +YT Y+Q ++ + + +M A V + + G LS Sbjct: 246 VILAFVSMMCAQGAVWYTSFFYVQTFMEKFLKVDPVTINELMMIATAVSAIFYVVFGWLS 305 Query: 304 DKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAA 339 DK+GR+ ML +LA +F P L+ ++P A Sbjct: 306 DKVGRKPVMLGGMTLALLFYFPGFHLLEKAANPALA 341 Score = 34.3 bits (77), Expect = 1e-05 Identities = 38/183 (20%), Positives = 71/183 (38%), Gaps = 10/183 (5%) Query: 249 LGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVF----MLIQPLIGALSD 304 L F G F T ++ L N +AN A+ A+ +L + G D Sbjct: 360 LQFDPVGKTAFVTSCDIVKSTLANAGVSYANEAAPAGAVAVMRIGGAEVLSKSAAGLGKD 419 Query: 305 KIGRRTSMLCFGSLAAIFT---VPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILK 361 ++ + T G + A P + ++ P L + + + + ++ L Sbjct: 420 EV-KATKAEVEGRIKAALAGAGYPTKADPARMNMPMILGVLFVFVIAATALFGPLAACL- 477 Query: 362 AEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVAFLVS 420 E+FP +VR + L Y + GG + A ++ ++G A WY +++ L + Sbjct: 478 VELFPTRVRYTALSLPYHIGTGWVGGFVPFFAFAIVAAVGNIYAGLWYPFAFTLLSVLTT 537 Query: 421 LML 423 L L Sbjct: 538 LFL 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: 630 Number of extensions: 31 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: 550 Length adjustment: 34 Effective length of query: 398 Effective length of database: 516 Effective search space: 205368 Effective search space used: 205368 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 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