Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 203 bits (517), Expect = 5e-57 Identities = 116/325 (35%), Positives = 185/325 (56%), Gaps = 20/325 (6%) Query: 2 VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 V + + V K + G+ + + ++N+ I GE +LGPSG+GKTT + ++AG + P+ GE Sbjct: 9 VLVSFRGVQKSYD-GENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGE 67 Query: 62 LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121 + R + + VPP R IGMVFQ +AL+P++T EN+AFPL+ +SK +I +RV Sbjct: 68 IQLAGRSINN-----VPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERV 122 Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181 + V ++ + +P +LSGGQQQRVALARALV +P L+L+DEP LD ++R+ + Sbjct: 123 KRVLSMVQLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQM 182 Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241 +K + RLGVT++ V+HD + ++DRV V +G++ Q+ P LY+ P + VA+ I Sbjct: 183 EIKHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFI 242 Query: 242 GEINELEGKVTN-----------EGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKD 290 GE N L G++ + G + +L V + +RPE V L+ Sbjct: 243 GENNRLNGRLHSHSGERCVVELARGEKVEALAVNVGQVGGPVTLSVRPERVSLNG---SS 299 Query: 291 DSWILVGKGKVKVIGYQGGLFRITI 315 +S + G+V Y G R+ + Sbjct: 300 ESCVNRFSGRVAEFIYLGDHVRVRL 324 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: 313 Number of extensions: 12 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: 370 Length adjustment: 29 Effective length of query: 324 Effective length of database: 341 Effective search space: 110484 Effective search space used: 110484 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