Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate AZOBR_RS22795 AZOBR_RS22795 spermidine/putrescine ABC transporter ATPase
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__azobra:AZOBR_RS22795 Length = 358 Score = 216 bits (550), Expect = 7e-61 Identities = 112/283 (39%), Positives = 179/283 (63%), Gaps = 17/283 (6%) Query: 16 GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75 G A+DNV + I+ GE +LGPSG GKTT +RI+AG + G + DR+V S Sbjct: 11 GASTAVDNVTLEIKAGELVALLGPSGCGKTTLLRILAGFQAQTLGRVVIGDRVVDS---- 66 Query: 76 IVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLN 135 +PP R +G+VFQ +AL+P++T +N+A+ L +++ +R RVE + ++ + + + Sbjct: 67 -LPPAGRGVGIVFQNYALFPHMTVAQNVAYGLEARGAARDAVRARVEAMLGLVKLDAMRD 125 Query: 136 HFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLL 195 FP++LSGGQQQRVALARAL PS+LLLDEPF+ LD +R + +K++Q R G+T + Sbjct: 126 RFPKQLSGGQQQRVALARALAIQPSILLLDEPFAALDKNLRLDMQIEIKQLQRRFGITTI 185 Query: 196 VVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVT--- 252 +V+HD + ++ADR+ VL +GKL Q G PED+YD P ++ V +G N+L G+V Sbjct: 186 MVTHDQEEALSMADRIAVLSRGKLEQFGTPEDVYDRPGTLFVNGFVGSANQLRGRVVRAS 245 Query: 253 --------NEGVVIGSLRFPVSVSS-DRAIIGIRPEDVKLSKD 286 G V+ ++ ++++ D AI+ +RPE+++L+ + Sbjct: 246 GSVAEVALEAGTVLSAVTPDAALAAGDPAILCVRPENLRLATE 288 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: 286 Number of extensions: 8 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: 358 Length adjustment: 29 Effective length of query: 324 Effective length of database: 329 Effective search space: 106596 Effective search space used: 106596 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