Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 169 bits (428), Expect = 1e-46 Identities = 91/241 (37%), Positives = 143/241 (59%), Gaps = 9/241 (3%) Query: 1 MAYLQLRGIEKFFGEHR--AIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGG 58 M+ LQL GI K F + + A+K I + I++G VG +G GK+TLL+LIAGLE D G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 59 SLMLDGRDITDQ----PSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKV 114 ++ G+ I + P+++R++ ++FQ YAL+P M++ EN+ AL + + I Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQI---A 117 Query: 115 QNAARILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRV 174 ++ + L P +LS GQRQR A+ RA+ PK+ L D+P +LD + + Sbjct: 118 MDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISE 177 Query: 175 EIAKLHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFI 234 +I + + G T I +H +A++LAD + +L GI++QVGTP+E+Y KPAN +VA F Sbjct: 178 DIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFF 237 Query: 235 G 235 G Sbjct: 238 G 238 Lambda K H 0.320 0.137 0.388 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: 237 Number of extensions: 7 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: 350 Length of database: 345 Length adjustment: 29 Effective length of query: 321 Effective length of database: 316 Effective search space: 101436 Effective search space used: 101436 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 (21.8 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