Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_090275379.1 BLU11_RS16790 TRAP transporter permease
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_900105005.1:WP_090275379.1 Length = 674 Score = 1178 bits (3048), Expect = 0.0 Identities = 579/674 (85%), Positives = 627/674 (93%) Query: 1 MSESQGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP 60 MSE +GL ASP++WPRALFYVALLFS YQIVTAAFHPVS+QVLRAGHVGFLLLLV+L YP Sbjct: 1 MSEDRGLSASPADWPRALFYVALLFSCYQIVTAAFHPVSTQVLRAGHVGFLLLLVYLSYP 60 Query: 61 ARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAAR 120 RGN +P+QP+AW+LGLAG ATF YQWYFEADLIQRSGD+TT DMVVG+ LI LVFEAAR Sbjct: 61 LRGNARPWQPLAWILGLAGMATFAYQWYFEADLIQRSGDLTTTDMVVGIILIALVFEAAR 120 Query: 121 RVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATY 180 RVMGIALPIIC LFLAYGL G +LPGDLAHRGYYLDQ+VNQLSFGTEGLYGTPTYVSATY Sbjct: 121 RVMGIALPIICGLFLAYGLFGNHLPGDLAHRGYYLDQVVNQLSFGTEGLYGTPTYVSATY 180 Query: 181 IFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT 240 IFLFILFGSFLEQAGMI+LFTDFAMGLFGHK GGPAKVSVVSSALMGTITGSGVANVVTT Sbjct: 181 IFLFILFGSFLEQAGMIRLFTDFAMGLFGHKAGGPAKVSVVSSALMGTITGSGVANVVTT 240 Query: 241 GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALI 300 GQFTIPLMKRFGYR AFAGGVEATSSMGSQIMPPVMGAVAFIMAETIN+P+VE+AKAAL+ Sbjct: 241 GQFTIPLMKRFGYRSAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINMPYVEVAKAALL 300 Query: 301 PALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTP 360 PALLYFGSVFWMVHLEA+R+ L GLPKDECPSA AAVK+RW+LLIPL VL+WLLFSGRTP Sbjct: 301 PALLYFGSVFWMVHLEARRSKLNGLPKDECPSAWAAVKQRWFLLIPLAVLIWLLFSGRTP 360 Query: 361 MFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALV 420 MFAGTIGLALTAIVILGSA+IL+VS+ A+R+ FW+ALG+LCAGFFQLGIGVIFGVI LV Sbjct: 361 MFAGTIGLALTAIVILGSALILRVSSTAIRLIFWVALGVLCAGFFQLGIGVIFGVIGVLV 420 Query: 421 AVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAV 480 A CWFIKGGRDTL+ICLHALVEGARHA+PVGIAC LVGVIIG+VSLTGVASTFAGYILA+ Sbjct: 421 AACWFIKGGRDTLLICLHALVEGARHAIPVGIACVLVGVIIGIVSLTGVASTFAGYILAI 480 Query: 481 GENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540 G++NLFLSLLLTMLTCL+LGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM Sbjct: 481 GQDNLFLSLLLTMLTCLMLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIM 540 Query: 541 ADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATL 600 ADLTPPVALACFAAAPIA+ GLKISMWAIRIA+AGF+VPFMAVYNPALMMQGGDW ATL Sbjct: 541 ADLTPPVALACFAAAPIARASGLKISMWAIRIAVAGFVVPFMAVYNPALMMQGGDWAATL 600 Query: 601 YMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLI 660 YMLFKAAFA+GLWG VFTGY + + WE L F A M+LA+PISDE+GFALGA+F+ Sbjct: 601 YMLFKAAFAIGLWGTVFTGYFMQRLTWWELPLGFVAGGLMILALPISDELGFALGAVFVA 660 Query: 661 QHIWRARRAEPATA 674 QH WRARRA A A Sbjct: 661 QHWWRARRALTAAA 674 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: 1767 Number of extensions: 84 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: 674 Length adjustment: 39 Effective length of query: 635 Effective length of database: 635 Effective search space: 403225 Effective search space used: 403225 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