Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 182 bits (461), Expect = 1e-50 Identities = 102/280 (36%), Positives = 160/280 (57%), Gaps = 7/280 (2%) Query: 9 VSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRL 68 +SK F + K A+ ++++ IE G I+G +G+GKTT +++IAGL+ P GE+ F + Sbjct: 9 ISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQT 68 Query: 69 VASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKIL 128 + NGK +P R++G++FQ +AL+P +T EN+ L + +I +A + Sbjct: 69 IV-NGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAMDSLALAGLE 127 Query: 129 DIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS 188 D + +P +LS GQ+QR ALARAL P LLLLD+PF +LD R ++ ++++ Sbjct: 128 DS---FSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVK 184 Query: 189 RLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELE 248 G+T +V SH D ++AD + +L KG L QVG P ++Y P + VA+ G+ NEL Sbjct: 185 ATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGKRNELL 244 Query: 249 GKVTNEGVV--IGSLRFPVSVS-SDRAIIGIRPEDVKLSK 285 T +G G + P S S +D+ I R ED K+ K Sbjct: 245 ATPTEDGFYAGFGFIPHPDSASYTDKVKILFRSEDAKIKK 284 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: 289 Number of extensions: 12 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: 345 Length adjustment: 29 Effective length of query: 324 Effective length of database: 316 Effective search space: 102384 Effective search space used: 102384 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