Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 207 bits (526), Expect = 5e-58 Identities = 114/311 (36%), Positives = 181/311 (58%), Gaps = 19/311 (6%) Query: 16 GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75 G+ + + ++N++I GE +LGPSG+GKTT + ++AG + P+ GE+ R + + Sbjct: 26 GESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGRSINN---- 81 Query: 76 IVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLN 135 VPP R IGMVFQ +AL+P++T EN+AFPLT +SK +I +RV+ V ++ + Sbjct: 82 -VPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDAFAK 140 Query: 136 HFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLL 195 +P +LSGGQQQRVALARALV +P L+L+DEP LD ++R+ + +K + RLGVT++ Sbjct: 141 RYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLGVTVV 200 Query: 196 VVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKV---- 251 V+HD + ++DRV V +G++ Q+ P LY+ P + VA+ IGE N + G + Sbjct: 201 YVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGENNRISGTLLASD 260 Query: 252 -------TNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGKGKVKVI 304 G + +L V + + + IRPE V+L+ +S + G+V Sbjct: 261 GKRCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRLNG---HSESCVNRFSGRVAEF 317 Query: 305 GYQGGLFRITI 315 Y G R+ + Sbjct: 318 IYLGDHVRVRL 328 Lambda K H 0.319 0.139 0.390 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: 322 Number of extensions: 10 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: 353 Length of database: 374 Length adjustment: 29 Effective length of query: 324 Effective length of database: 345 Effective search space: 111780 Effective search space used: 111780 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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