Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 192 bits (488), Expect = 1e-53 Identities = 111/290 (38%), Positives = 173/290 (59%), Gaps = 17/290 (5%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M I + NVS+ + G V A+D+V+ +E G +LGPSG GK+T +R+IAGL+ ++G Sbjct: 1 MSAIQLLNVSRHW--GDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSG 58 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 + +R V +PP R++ MVFQ++AL+P+LT ENI F LT K+ + E KR Sbjct: 59 RIMIGERDVTH-----LPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKR 113 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 + IL + +L P ELSGGQQQRVAL RALV + ++ L+DEP SNLDA++R R Sbjct: 114 LTRAVDILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMR 173 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 ++ +Q LG+T++ V+HD + ++ADR+ ++ G++VQ P +LY P + + Sbjct: 174 REIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNF 233 Query: 241 IG-------EINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKL 283 IG +++ G V G G++ V S ++GIRPE +++ Sbjct: 234 IGTPPMNLVRLDDARGSVCVAGSRSGTVSV---VDSADYVLGIRPEHIRI 280 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: 278 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: 350 Length adjustment: 29 Effective length of query: 324 Effective length of database: 321 Effective search space: 104004 Effective search space used: 104004 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