Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 145 bits (366), Expect = 1e-39 Identities = 90/297 (30%), Positives = 153/297 (51%), Gaps = 5/297 (1%) Query: 39 IVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAF 98 ++ +V+F+ +S HF+S LA I + +++ M F L DLSVGS +A Sbjct: 33 LLAMIVLFSFLS---SHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLAL 89 Query: 99 AGVLCAMVLNATG-NTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLG 157 A ++ + G + + +A + G + G V RI + I +L +E+ RGL Sbjct: 90 AASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLA 149 Query: 158 FIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGN 217 + + + + D + FGVS + LL ++ ++L +TV+GR + IG N Sbjct: 150 YQFTDSRTAYIG-DAYAWFSNPVAFGVSPAFIIALLVIVLAQLVLTRTVFGRYLIGIGTN 208 Query: 218 PEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISACVLGG 277 EA RLAGI+ +V +F + G + LA + SR+ + PNA G EL VI+A V+GG Sbjct: 209 EEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVIGG 268 Query: 278 VSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNR 334 SL+GGR ++ GVLI+ + + + + ++ GA+++ AV+LD ++R Sbjct: 269 TSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYRSR 325 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: 281 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 331 Length adjustment: 28 Effective length of query: 310 Effective length of database: 303 Effective search space: 93930 Effective search space used: 93930 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: 49 (23.5 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