Align Alpha-ketoglutarate permease (characterized)
to candidate CCNA_01071 CCNA_01071 alpha-ketoglutarate permease
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__Caulo:CCNA_01071 Length = 477 Score = 395 bits (1015), Expect = e-114 Identities = 209/470 (44%), Positives = 293/470 (62%), Gaps = 47/470 (10%) Query: 6 VTADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQT 65 +TA ++ T R AI+G S+GNLVEW+D++ Y+ +LYFA FFP G+ T QLLQ Sbjct: 1 MTATTEATRLTPVARARAILGGSAGNLVEWYDWFAYAAFTLYFAPAFFPKGDQTVQLLQA 60 Query: 66 AGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPA 125 A VF GF+ RPIG W+ G AD GR+ ++ +SV +MC G+ +IA P ++TIG WAPA Sbjct: 61 AAVFFLGFVARPIGAWIMGLYADHAGRRAALSVSVSLMCAGAFIIAITPDFQTIGLWAPA 120 Query: 126 LLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQH 185 +LL AR+ QGLSVGGEYG SATYMSE+A + R+GF++SF YVTLI GQLLAL V+++LQ Sbjct: 121 ILLFARVLQGLSVGGEYGASATYMSEMAGKARRGFWSSFHYVTLIAGQLLALGVLIILQR 180 Query: 186 TMEDAALREWGWRIPFALGAVLAVVALWLRRQLDET------SQQETRA----------- 228 T+ + AL+EW WR+PF +GA+LAVV W+RR L+E+ +Q ET + Sbjct: 181 TLGEEALKEWAWRVPFIIGALLAVVVFWIRRGLEESVSFKRPAQSETLSRGQIISAGAFL 240 Query: 229 ---------------LKEAGSLKG---------------LWRNRRAFIMVLGFTAAGSLC 258 L +AG G + R+ R ++++G TA GSL Sbjct: 241 SLTIASGVVGLMGGPLAKAGQYLGAAFLVLFFVSLIVPLIRRHPRESLLIMGLTAGGSLT 300 Query: 259 FYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRTSMLCFGSL 318 FY +TTYMQK+LVNTAG AS I +L FML+QPL G LSD+ GR+ ++ Sbjct: 301 FYVYTTYMQKFLVNTAGFSKAQASEISALSLIAFMLMQPLAGWLSDRFGRKPMLIIAFGG 360 Query: 319 AAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSY 378 + PI++A+ +S A L++ + S YT+IS ++KAEMFPA++RALGV L Y Sbjct: 361 GVLTIWPIMTAISQTNSVGVALALILVGVAFQSCYTAISAVVKAEMFPAEIRALGVALPY 420 Query: 379 AVANAIFGGSAEYVALSLKSIGMETAFFWYVTLMAVVAFLVSLMLHRKGK 428 A+AN +FGG+AE VAL+ K +E+ F+ YV + + + S++L G+ Sbjct: 421 ALANVLFGGTAEMVALAFKHENLESTFYVYVAAVMTIGLICSIILKDTGR 470 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: 586 Number of extensions: 28 Number of successful extensions: 3 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: 477 Length adjustment: 33 Effective length of query: 399 Effective length of database: 444 Effective search space: 177156 Effective search space used: 177156 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