Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate CA265_RS04175 CA265_RS04175 phosphonate ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Pedo557:CA265_RS04175 Length = 232 Score = 139 bits (349), Expect = 9e-38 Identities = 84/220 (38%), Positives = 129/220 (58%), Gaps = 5/220 (2%) Query: 4 IIVKNVSKVFKKGKV--VALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 I ++N+ KV+K +V AL+ +N+++ GE I+GPSG GK+T + ++ LD P G Sbjct: 2 IKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENGS 61 Query: 62 LYF-DDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 F D L+ N + R +G VFQ + L LT FENI PL K+ E +K Sbjct: 62 YKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIELPLIYNKIPAGERKKL 121 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V E+ + ++I + HFP++LSGGQQQRVA+ARALV P L+L DEP NLD+ + Sbjct: 122 VNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEVM 181 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLV 220 L+ E+ + G T+++V+H D + ++R+ L G ++ Sbjct: 182 ELLCEL-NETGTTIVMVTHSSHDA-SFSNRIINLKDGHVI 219 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: 197 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: 232 Length adjustment: 26 Effective length of query: 327 Effective length of database: 206 Effective search space: 67362 Effective search space used: 67362 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: 47 (22.7 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