Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 125 bits (314), Expect = 4e-33 Identities = 103/338 (30%), Positives = 161/338 (47%), Gaps = 13/338 (3%) Query: 10 FGAAQAGAQSQLALPASRGKRA---RSELARLRELALLPALALLIVIGAFISPSFLTKAN 66 F + A + A PA+ A RS+L L LL LA ++ + + +S F + Sbjct: 558 FSCDRMNAPTAPAAPAATPSSASVWRSQLGTY--LGLLAVLAGMVALFSSLSEYFWSAET 615 Query: 67 LISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPA 126 I++ ALA++ + + +++ DLS+ S + +A A A AA +G PA Sbjct: 616 FITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSA-----AAILQWGWTVPA 670 Query: 127 AAGLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSF 186 AA L + G V G I G + V RL +FIV+L ML +RG T T + + + Sbjct: 671 AAALA--LATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQY-VGDAI 727 Query: 187 FALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITW 246 L+ G+ + LA +A +L GR + IG N EA R AG+ I Sbjct: 728 SWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRV 787 Query: 247 GVFVLGSILASVGGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTG 306 VF + +LA + GL+ + + A + N G GM V AA VIGG SL GG+G++ G Sbjct: 788 IVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFG 847 Query: 307 VLLLGVVQNLLTLAQVPSFWIQAIYGAIILGSLMVARL 344 VL++ V++ L + I G +I+ +++V L Sbjct: 848 VLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTL 885 Lambda K H 0.326 0.140 0.397 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: 520 Number of extensions: 25 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: 351 Length of database: 892 Length adjustment: 36 Effective length of query: 315 Effective length of database: 856 Effective search space: 269640 Effective search space used: 269640 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 (21.6 bits) S2: 53 (25.0 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