Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 176 bits (445), Expect = 1e-48 Identities = 101/273 (36%), Positives = 159/273 (58%), Gaps = 11/273 (4%) Query: 21 LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPE 80 L +++ + GE +LGPSG GKTT ++ IAGL S G + + RL+ S + VP E Sbjct: 19 LRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLL-SGPETFVPSE 77 Query: 81 DRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRE 140 R++GM+FQ +AL+P+LT ENI F + + K + R+ E+ ++ + + +P E Sbjct: 78 RREVGMIFQDYALFPHLTVAENILFGVKGL--DKAARQARLGEMLALVKLEGLGGRYPHE 135 Query: 141 LSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHD 200 LSGGQQQRV++ARAL +P LLLLDEPFSN+DA++R ++E+ + GV+ + V+H Sbjct: 136 LSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVFVTHS 195 Query: 201 PADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVVIGS 260 + F AD++ + G + Q G E LY P VA +G++N L +V + + + Sbjct: 196 KDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQVNYLSCEV-KDRARLQT 254 Query: 261 LRFPVSVSSD-------RAIIGIRPEDVKLSKD 286 L V SSD R + +RPE ++++ D Sbjct: 255 LLGEVQSSSDLPKAAGYRGELLLRPEQLQMAGD 287 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: 281 Number of extensions: 15 Number of successful extensions: 3 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: 342 Length adjustment: 29 Effective length of query: 324 Effective length of database: 313 Effective search space: 101412 Effective search space used: 101412 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