Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 203 bits (517), Expect = 5e-57 Identities = 123/332 (37%), Positives = 195/332 (58%), Gaps = 31/332 (9%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + ++NV+K + G+VV ++N++I GE +GPSG GK+T +R+IAGL+ ++G Sbjct: 1 MASVQLQNVTKAW--GEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 +L+ ++ + PP +R +GMVFQ++ALYP+L+ EN++F L KE I +R Sbjct: 59 DLFIGEKRMNDT-----PPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V +VA++L + H+L+ P+ LSGGQ+QRVA+ R LV +PS+ LLDEP SNLDA +R R Sbjct: 114 VNQVAEVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 + + RLG T++ V+HD + +AD++ VL G++ QVGKP +LY P VA Sbjct: 174 IEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGF 233 Query: 241 IG--EINELEGKVTNEGVVIGSLRFP---------------VSVSSDRAIIGIRPEDVKL 283 IG ++N L KVT + + P V V ++ + +GIRPE Sbjct: 234 IGSPKMNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMS-LGIRPE---- 288 Query: 284 SKDVIKDDSWILVGKGKVKVIGYQGGLFRITI 315 ++ D ++ +G+V+V+ G +I I Sbjct: 289 --HLLPSDIADVILEGEVQVVEQLGNETQIHI 318 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: 283 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: 371 Length adjustment: 29 Effective length of query: 324 Effective length of database: 342 Effective search space: 110808 Effective search space used: 110808 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