Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_068175283.1 HTA01S_RS21950 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_001592305.1:WP_068175283.1 Length = 677 Score = 900 bits (2327), Expect = 0.0 Identities = 452/676 (66%), Positives = 540/676 (79%), Gaps = 2/676 (0%) Query: 1 MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60 MS S A+F+VA+ FS YQ+ A+FHP+SSQV+R+ HVGF+LL++F +P Sbjct: 1 MSNQSSSETPTSPLRGAIFWVAIAFSAYQLWMASFHPLSSQVIRSIHVGFVLLMIFALFP 60 Query: 61 AR-GNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAA 119 G ++ + WLLGLAGFAT YQW FEADL R+G++T AD VVG+ LI LVFEAA Sbjct: 61 PMDGRSGAWRALGWLLGLAGFATGLYQWVFEADLTLRAGELTQADWVVGVLLITLVFEAA 120 Query: 120 RRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSAT 179 RRVMG LP++C FL Y L G++LPG LAHRGY +DQ+V+ L FGTEGLYGTPTYVS+T Sbjct: 121 RRVMGWGLPLVCLTFLLYALFGQHLPGALAHRGYGMDQVVSTLGFGTEGLYGTPTYVSST 180 Query: 180 YIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVT 239 YIFLFILFG+FLEQAGMI LF DFAMG GH GGPAKVSV+SS LMGTI GSGVANVVT Sbjct: 181 YIFLFILFGAFLEQAGMIGLFNDFAMGTVGHTRGGPAKVSVISSGLMGTINGSGVANVVT 240 Query: 240 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL 299 TGQFTIPLMKRFGY PAFAGGVEAT+SMG QIMPPVMGAVAFIMAETINVP+++I KAAL Sbjct: 241 TGQFTIPLMKRFGYSPAFAGGVEATASMGGQIMPPVMGAVAFIMAETINVPYIDIVKAAL 300 Query: 300 IPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRT 359 IPA+LYF + FWMVHLEA R GL GLPKDECP+ AAV+ERWYLL+PL+ LV LLFSG T Sbjct: 301 IPAILYFVTAFWMVHLEAGRKGLMGLPKDECPNPWAAVRERWYLLLPLMGLVALLFSGYT 360 Query: 360 PMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAAL 419 P+F+GT+GL LTAI+I G+A+I V ALR W+ LG CAGFFQ G+GV F + A L Sbjct: 361 PLFSGTVGLGLTAILIFGAAVISGVKPIALRGLAWVLLGFACAGFFQFGVGVFFVITALL 420 Query: 420 VAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILA 479 VA+ + ++ G D + + ALV+GARHA+PV IACALVGVIIGV++LTGVA+ GYI+A Sbjct: 421 VAMTFVLRTGGDARALAVKALVDGARHALPVAIACALVGVIIGVINLTGVAAELGGYIIA 480 Query: 480 VGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI 539 +G ++LFL+LLLTM+TCLVLGMGIPTIPNYIITSS+AAP LL+LGVPLIVSHMFVFYFGI Sbjct: 481 IGRDSLFLALLLTMVTCLVLGMGIPTIPNYIITSSLAAPVLLELGVPLIVSHMFVFYFGI 540 Query: 540 MADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGAT 599 MADLTPPVALACFAAAPIA+E GLKIS+ AIR+AIAGFIVPFMAVY+PALM+Q GDW T Sbjct: 541 MADLTPPVALACFAAAPIARESGLKISVQAIRVAIAGFIVPFMAVYSPALMLQSGDWMDT 600 Query: 600 LYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFL 659 +++FKA A+ +WGA GYL P+ E+ LA AA+ +++A+P++DEIG A F+ Sbjct: 601 TWIVFKALVAIAMWGAGAIGYLAGPLNWVERALAIVAASFLIVALPLTDEIGLGAVAAFV 660 Query: 660 IQHIWRAR-RAEPATA 674 H+WR R R ATA Sbjct: 661 AWHLWRTRQRRAMATA 676 Lambda K H 0.330 0.143 0.445 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: 1669 Number of extensions: 83 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: 674 Length of database: 677 Length adjustment: 39 Effective length of query: 635 Effective length of database: 638 Effective search space: 405130 Effective search space used: 405130 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: 54 (25.4 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