Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate AZOBR_RS16500 AZOBR_RS16500 C4-dicarboxylate ABC transporter permease
Query= reanno::psRCH2:GFF84 (674 letters) >FitnessBrowser__azobra:AZOBR_RS16500 Length = 673 Score = 402 bits (1032), Expect = e-116 Identities = 255/686 (37%), Positives = 361/686 (52%), Gaps = 83/686 (12%) Query: 23 LLFSIYQIVTAAFHPVSSQVLRAGHVGFLLLLVFLCYP--ARGNGKP-----FQPVA--- 72 ++ S++ TA F + R H+ F+L LVFL +P RG G+P +P+ Sbjct: 37 IILSLFHYYTAGFGLLPEMEHRGIHLSFVLGLVFLVFPFTKRGYGEPVMGTLLRPLGIGL 96 Query: 73 --WLLGLAGFATFFYQWYFEAD-LIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPI 129 W L + + D L R G+ TT D+++G LI+++ EA RR +G LPI Sbjct: 97 QDWALAIGAVVAVMHVPLIPLDDLAFRVGNPTTTDVILGSILIIVLLEATRRSVGWPLPI 156 Query: 130 ICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGS 189 I +F++Y + G +PG L H G + Q+V+ L T+G+YG V ATY+F F+LFG Sbjct: 157 ISLIFMSYAIWGPQMPGLLKHPGATVSQLVDHLYLTTQGVYGIALGVVATYVFHFVLFGV 216 Query: 190 FLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMK 249 F + G+ +LF D A + G GGPAKV++ SAL G I+GS VAN VT G TIP MK Sbjct: 217 FATRIGLGQLFLDCAAWVAGRYAGGPAKVAIFGSALFGMISGSSVANTVTVGSLTIPAMK 276 Query: 250 RFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSV 309 R GY+P FA VE+T+S G QI PP+MGA AF+M E + +P+ I AA++PA ++F V Sbjct: 277 RMGYKPHFAAAVESTASTGGQITPPIMGAAAFLMIEFLGLPYTTIIMAAIVPAFMHFFGV 336 Query: 310 FWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLA 369 VH EAKR GL+GL DE P A + W +IPLVVL+ +L +G TP A G+ Sbjct: 337 LVQVHFEAKRNGLRGLRPDEMPDLKEAFRRDWPTVIPLVVLIGILIAGYTPYMAAFWGIT 396 Query: 370 LTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGG 429 L I + + N R+ W L G Sbjct: 397 L--------CIAVGLLNPRKRMTIWEVL-----------------------------DGL 419 Query: 430 RDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGV-------------------A 470 RD GA++A+ VG A A VG+I+GVV+LTGV Sbjct: 420 RD-----------GAKYALAVGAAAATVGIIVGVVTLTGVGFKISYIVTSTAGEMAVWAG 468 Query: 471 STFAGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVS 530 + G++ L +L++T + C+++G GIPT NYII ++IAAPAL LGV IV+ Sbjct: 469 AFLPGWLADAKALTLLFTLIMTGVVCILMGCGIPTTANYIIMATIAAPALGLLGVAPIVA 528 Query: 531 HMFVFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALM 590 H FVFY+G++AD+TPPVALA +AAA +A K A R+ +A +VPF+ V++P+L+ Sbjct: 529 HFFVFYYGVLADITPPVALAAYAAAGMAGADPFKTGNTAFRLGLAKALVPFVFVFSPSLL 588 Query: 591 M--QGGDWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASMVLAMPISD 648 + G +W + GA TG+L M WE++L AA +V S Sbjct: 589 LVAPGFNWPDFFIAFLGCIVGIVCLGATLTGWLLTNMRGWERLLLGIAAILLVTPELYSS 648 Query: 649 EIGFALGALFLIQHIWRARRAEPATA 674 +G AL L++ + ARR P A Sbjct: 649 LLGLALIVPVLLRQM-SARRLMPEAA 673 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: 1401 Number of extensions: 95 Number of successful extensions: 4 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: 673 Length adjustment: 39 Effective length of query: 635 Effective length of database: 634 Effective search space: 402590 Effective search space used: 402590 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