Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 168 bits (425), Expect = 6e-46 Identities = 106/325 (32%), Positives = 174/325 (53%), Gaps = 5/325 (1%) Query: 15 AAEALIPQSNDKAKWWQQITEY-SLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIG 73 AA A P S + W Q+ Y L+ + M A S ++F+S E + +A I + Sbjct: 570 AAPAATPSS--ASVWRSQLGTYLGLLAVLAGMVALFSSLSEYFWSAETFITIANEIPALA 627 Query: 74 MVSCTMMFCLASRDFDLSVGSTVAFAGVLCAMVLNATGNTFIAIVA-AVAAGGVIGFVNG 132 +++ M F L DLSVGS +A A A + G T A A A+A G V G + G Sbjct: 628 VMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVPAAAALALATGLVCGTITG 687 Query: 133 AVIAYLRINALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTL 192 A+ R+ + I +L +E VRG ++V+ + V D L F G+S + + Sbjct: 688 AISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQYVG-DAISWLSAPFFGGISFAFLLAV 746 Query: 193 LCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILAS 252 + +V ++L++TV+GR + IG N EA RLAG++ RV +F + G + LAG++ ++ Sbjct: 747 VLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSA 806 Query: 253 RITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAF 312 R+ + PNA G EL VI+A V+GG SL+GGR ++ GVLI+ +E + + Sbjct: 807 RLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEP 866 Query: 313 YQYLVRGAILLAAVLLDQLKNRGSR 337 + ++ G +++AAV++D L+ R ++ Sbjct: 867 SKRIITGFVIVAAVIVDTLRQRRAK 891 Lambda K H 0.326 0.139 0.396 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: 586 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: 338 Length of database: 892 Length adjustment: 35 Effective length of query: 303 Effective length of database: 857 Effective search space: 259671 Effective search space used: 259671 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 (21.7 bits) S2: 52 (24.6 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