Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 206 bits (523), Expect = 1e-57 Identities = 119/296 (40%), Positives = 179/296 (60%), Gaps = 15/296 (5%) Query: 2 VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 VR++ NV+K F G V A+D++N+ I GE F +LGPSG GKTT +R++AG + GE Sbjct: 4 VRLV--NVTKRF--GGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGE 59 Query: 62 LYFDDRLV-ASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 ++ DRL+ A +PPE R GMVFQ +A++P+L+ +EN+AFPL ++S EI +R Sbjct: 60 IHVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRR 119 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 E + V P +LSGG +QRVALARAL +P ++LLDEP S+LD +R+ R Sbjct: 120 TREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMR 179 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 +K++Q G ++L V+HD ++ A++DR+ V+ G + QVG P D+Y NP + V Sbjct: 180 FEIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGF 239 Query: 241 IGEINELEGKVTNEGVVI---GSLRFPVS-------VSSDRAIIGIRPEDVKLSKD 286 IG N L+ +T EG+V G R + VS+ RA + RP ++ + + Sbjct: 240 IGLSNFLDVNLTPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEIDFTAE 295 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: 295 Number of extensions: 9 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: 354 Length adjustment: 29 Effective length of query: 324 Effective length of database: 325 Effective search space: 105300 Effective search space used: 105300 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 Apr 09 2024. 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