Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate AO353_29310 AO353_29310 transporter
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29310 Length = 380 Score = 204 bits (518), Expect = 4e-57 Identities = 116/319 (36%), Positives = 180/319 (56%), Gaps = 21/319 (6%) Query: 5 IVKNVSKVFKK-GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 ++ V +V KK + +A+D+V+++I GE F +LG SG+GK+T +R++AG + P+ G +Y Sbjct: 21 VLVRVDRVTKKFDETIAVDDVSLDIHQGEIFAMLGGSGSGKSTLLRMLAGFERPTEGRIY 80 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123 D + +PP +R I M+FQ++AL+P++T +NIAF L ++ EI RVEE Sbjct: 81 LDGVDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDRLPASEIEARVEE 135 Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183 + K++ + P +LSGGQ+QRVALAR+L K P LLLLDEP LD ++R + + Sbjct: 136 MLKLVHMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLEL 195 Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243 E+ R+GVT ++V+HD + +A R+ ++ G + Q+G P D+Y+ PVS V IG Sbjct: 196 VEIIERVGVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYEAPVSRMVCEFIGN 255 Query: 244 INELEGKVTNEGVVIGSLRFP-------------VSVSSDRAIIGIRPEDVKLSKDVIKD 290 +N +G V + + P SV IRPE K+ +K Sbjct: 256 VNAFDGTVVEDLEGHAIIHSPDLEQKIYVGHGVSTSVQDKSITYAIRPE--KMLVSTLKP 313 Query: 291 DSWILVGKGKVKVIGYQGG 309 D+ +GKV I Y GG Sbjct: 314 DTRYNWSQGKVHDIAYLGG 332 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: 297 Number of extensions: 11 Number of successful extensions: 2 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: 353 Length of database: 380 Length adjustment: 30 Effective length of query: 323 Effective length of database: 350 Effective search space: 113050 Effective search space used: 113050 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