Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_011383333.1 AMB_RS04540 C4-dicarboxylate ABC transporter
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_000009985.1:WP_011383333.1 Length = 687 Score = 803 bits (2075), Expect = 0.0 Identities = 394/654 (60%), Positives = 494/654 (75%), Gaps = 1/654 (0%) Query: 16 RALFYVALLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYPARGNGKPFQ-PVAWL 74 R +F++A+ FS++QIVTAA+ P+SS +R+ HVGFLLL+VF Y A G G P + AW Sbjct: 28 RGIFWIAIAFSVFQIVTAAYSPLSSLPVRSIHVGFLLLMVFALYAAMGRGNPVKVATAWA 87 Query: 75 LGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIICALF 134 LG F Y +E +L+QRSGD +T D+VVG ++ LVFEAARR+MG ALP +C +F Sbjct: 88 LGGLSFILSLYHLIYEGELVQRSGDPSTTDLVVGTVMVALVFEAARRLMGWALPALCLVF 147 Query: 135 LAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFLEQA 194 +AY GE LP L HRGY DQI+NQ GTEG++G P YVSATYIFLFILFGSFLEQA Sbjct: 148 VAYAAFGEILPAPLGHRGYGFDQIINQYFLGTEGIFGIPCYVSATYIFLFILFGSFLEQA 207 Query: 195 GMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRFGYR 254 GMI+LFTD A+G GH GGPAKV+VV+S LMGTI GSG+ANVVTTG TIPLMKRFGYR Sbjct: 208 GMIRLFTDVALGTVGHTKGGPAKVAVVTSGLMGTINGSGIANVVTTGALTIPLMKRFGYR 267 Query: 255 PAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFWMVH 314 FAG VEAT+SMG QIMPPVMGAVAFIMAET+N+ + E+ KAA IPALLY+ S WMVH Sbjct: 268 SEFAGAVEATASMGGQIMPPVMGAVAFIMAETLNISYAEVCKAAAIPALLYYASAIWMVH 327 Query: 315 LEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLALTAIV 374 LEA AGL G+PKD+CPSA A++ +WYL++PL LV+LL +G TPMF+GT+GLALTAIV Sbjct: 328 LEAGIAGLHGMPKDQCPSAQGALRRQWYLMVPLAALVYLLLAGFTPMFSGTVGLALTAIV 387 Query: 375 ILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGGRDTLV 434 ILGS+I + A R+ FW LG+ + FF+LGI V+ +A LV V +F++GGR+T+ Sbjct: 388 ILGSSIAANIGGMAGRVVFWGVLGIASSAFFKLGINVVVVTVAVLVGVNFFVRGGRETMR 447 Query: 435 ICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLTML 494 + + LVEGAR AVPVG+AC LVG IIG ++LTG+A +F ++++ +LFL+L+LTM+ Sbjct: 448 MTVRGLVEGARSAVPVGVACTLVGTIIGTMTLTGIAGSFTQGLVSMSGGSLFLTLILTMI 507 Query: 495 TCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVALACFAA 554 L+LGMGIPTIP YIITSS+ AP L +GVPL+VSHM+VFYFGI+ADLTPPV LA FAA Sbjct: 508 ASLILGMGIPTIPTYIITSSLVAPMLFKMGVPLVVSHMYVFYFGILADLTPPVGLAAFAA 567 Query: 555 APIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYMLFKAAFAVGLWG 614 A IA+ WA+R+A+AGF+VPFMAVY+P+LMM G T Y++ KA A+GLWG Sbjct: 568 ASIARSNFFVTGWWAVRVAMAGFVVPFMAVYDPSLMMVSGSLFDTAYVVIKALLAIGLWG 627 Query: 615 AVFTGYLQRPMALWEKVLAFAAAASMVLAMPISDEIGFALGALFLIQHIWRARR 668 A GYL PM +WE+ +A AA +V A+P++DEIGFAL A+FL H RARR Sbjct: 628 AATIGYLWAPMKMWERAVAVLAAFLLVAAVPLTDEIGFALSAVFLAWHWMRARR 681 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: 1492 Number of extensions: 74 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: 687 Length adjustment: 39 Effective length of query: 635 Effective length of database: 648 Effective search space: 411480 Effective search space used: 411480 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