Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 151 bits (382), Expect = 2e-41 Identities = 82/241 (34%), Positives = 137/241 (56%), Gaps = 7/241 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+ L+L ++K + +K+I ++I++G +VG +G GK+TL+ IAGLE G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 61 AILVDDADI----SGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116 I+ I S + R++ ++FQ YAL+P M++ +N+ L +I + Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAMDS 120 Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 ++ L E S P QLS GQ+QR A+ RALA RPK+ L D+P +LD + + E+ Sbjct: 121 LALAGL---EDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISE 177 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 +++ + + T + +H +A++L D +A++ GI+QQ GTP +IY PAN +VA+F Sbjct: 178 DIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFF 237 Query: 237 G 237 G Sbjct: 238 G 238 Lambda K H 0.319 0.138 0.393 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: 300 Number of extensions: 10 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: 386 Length of database: 345 Length adjustment: 30 Effective length of query: 356 Effective length of database: 315 Effective search space: 112140 Effective search space used: 112140 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