Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate 7023222 Shewana3_0456 TRAP transporter, 4TM/12TM fusion protein (RefSeq)
Query= reanno::psRCH2:GFF84 (674 letters) >FitnessBrowser__ANA3:7023222 Length = 677 Score = 1092 bits (2824), Expect = 0.0 Identities = 533/669 (79%), Positives = 606/669 (90%), Gaps = 1/669 (0%) Query: 1 MSES-QGLHASPSEWPRALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCY 59 MS+S QGL A S+WP+ALFY AL+FSI+QI+TAAFHPVS+QVLRA HVGFLLL+VFL Y Sbjct: 1 MSDSEQGLGAKTSDWPKALFYTALVFSIFQIITAAFHPVSTQVLRATHVGFLLLIVFLSY 60 Query: 60 PARGNGKPFQPVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAA 119 PA G +P+QP+ W+LGLAG AT YQW+FEADLIQRSG++T ADMV+G+ LIVLVFEAA Sbjct: 61 PAVGKSRPWQPLGWVLGLAGMATAAYQWFFEADLIQRSGELTDADMVIGVVLIVLVFEAA 120 Query: 120 RRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSAT 179 RRVMG ALPIIC +FLAYGL G+YLPGDL HRGY +DQI+NQLSFGTEGLYGTPTYVSAT Sbjct: 121 RRVMGWALPIICCIFLAYGLFGQYLPGDLMHRGYGVDQIINQLSFGTEGLYGTPTYVSAT 180 Query: 180 YIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVT 239 YIFLFILFG+FLEQAGMI+LFTDFAMGLFGHKLGGPAKV+VVSSA+MGTITGSGVANVVT Sbjct: 181 YIFLFILFGAFLEQAGMIRLFTDFAMGLFGHKLGGPAKVAVVSSAMMGTITGSGVANVVT 240 Query: 240 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL 299 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPP+MGAVAFIMAETINVPF+EIAKAAL Sbjct: 241 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPIMGAVAFIMAETINVPFIEIAKAAL 300 Query: 300 IPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRT 359 IPALLYF SVFWMVHLEAKRA L GLPKD+CP AAVKERWYLLIPL +L++LLFSGRT Sbjct: 301 IPALLYFSSVFWMVHLEAKRANLCGLPKDQCPDPWAAVKERWYLLIPLFILIYLLFSGRT 360 Query: 360 PMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAAL 419 P+F+G +GLALT+IVILGSAI+L++ + A+R AFWIALG+LCAGFFQ+GI V+FGVIA L Sbjct: 361 PLFSGMVGLALTSIVILGSAIVLRLPSNAMRFAFWIALGVLCAGFFQMGIAVVFGVIALL 420 Query: 420 VAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILA 479 VAVCWFIKGG+DTL ICLHALV+GARHAVPVGIACALVGVIIG+VSLTG+ASTFA YILA Sbjct: 421 VAVCWFIKGGKDTLTICLHALVDGARHAVPVGIACALVGVIIGIVSLTGIASTFASYILA 480 Query: 480 VGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI 539 VG++NLFLSL+LTMLTC+VLGMGIP+IPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI Sbjct: 481 VGQDNLFLSLVLTMLTCMVLGMGIPSIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGI 540 Query: 540 MADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGAT 599 MADLTPPVALACFAAAPIAKE GLKIS+WAIRIAIAGF++PFMAVY PALM+Q W A Sbjct: 541 MADLTPPVALACFAAAPIAKESGLKISLWAIRIAIAGFVIPFMAVYEPALMLQSDSWLAI 600 Query: 600 LYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFL 659 +++ KA +G+WG +FTG+L + + WE+V+ F A AS++LA P+SDEIGF L LF+ Sbjct: 601 GFVMLKATVGIGIWGVIFTGFLLQKLYWWERVIGFLAGASLILATPLSDEIGFGLALLFI 660 Query: 660 IQHIWRARR 668 +QH R R+ Sbjct: 661 VQHSLRVRK 669 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: 1701 Number of extensions: 81 Number of successful extensions: 2 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 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