Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 196 bits (498), Expect = 7e-55 Identities = 115/286 (40%), Positives = 168/286 (58%), Gaps = 22/286 (7%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M + + NV K F GK + V+I++ GE I+GPSG GK+T +R++AGL+ S+G Sbjct: 1 MATLTLDNVKKSF--GKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 E+ D R+V + + P DR I MVFQ +ALYP+++ F+N+A+ L K+ K EI R Sbjct: 59 EVRIDGRVVNT-----LEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V AK+L + L P+ELSGGQ+QRVA+ RA+V+ P++ L DEP SNLDA++R R Sbjct: 114 VAVAAKLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 +K +Q LGVT L V+HD + +ADR+ V+ G Q+G P ++Y NP + VA Sbjct: 174 LEIKALQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGF 233 Query: 241 IGE--INELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLS 284 IG N L + G P +GIRPE ++++ Sbjct: 234 IGSPPTNFLPADMVRAG--------PAGQQ-----VGIRPEHLRVA 266 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: 255 Number of extensions: 11 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: 333 Length adjustment: 29 Effective length of query: 324 Effective length of database: 304 Effective search space: 98496 Effective search space used: 98496 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