Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 150 bits (379), Expect = 4e-41 Identities = 94/301 (31%), Positives = 156/301 (51%), Gaps = 6/301 (1%) Query: 39 IVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAF 98 ++ +V+F+ +S HF S + LA I + +++ M F L DLSVGS +A Sbjct: 27 LLAMIVLFSVLS---SHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLAL 83 Query: 99 AGVLCAMVLNATG-NTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLG 157 A ++ + G A + +A + G + G++ RI + I +L +E+ RG+ Sbjct: 84 AASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGVA 143 Query: 158 FIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGN 217 + ++ G D F L FG+S + LL V +L +TV+GR + IG N Sbjct: 144 YQMT-GSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFVAQAVLTRTVFGRYLIGIGTN 202 Query: 218 PEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISACVLGG 277 EA RLAGIN + +V +F + G + +A + SR+ + PNA G EL VI+A V+GG Sbjct: 203 EEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGG 262 Query: 278 VSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKN-RGS 336 SL+GGR ++ GVLI+ + + + + ++ GA+++ AV+LD ++ R S Sbjct: 263 TSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQRAS 322 Query: 337 R 337 R Sbjct: 323 R 323 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: 294 Number of extensions: 16 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: 325 Length adjustment: 28 Effective length of query: 310 Effective length of database: 297 Effective search space: 92070 Effective search space used: 92070 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