Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_010961191.1 MCA_RS09520 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_000008325.1:WP_010961191.1 Length = 356 Score = 206 bits (525), Expect = 6e-58 Identities = 122/296 (41%), Positives = 172/296 (58%), Gaps = 7/296 (2%) Query: 29 GKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPAEN 88 G + L L I +GE L ++GPSGCGK+T+LRLIAGL+ +G I + D+ + Sbjct: 16 GFAALSDLSLDIADGELLVVVGPSGCGKSTLLRLIAGLDRPTAGSIRIGGTDVNALAPAE 75 Query: 89 RYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQL 148 R V VFQ YAL+P+MTV N+ F L+M++ AE R+ + M++L R+P QL Sbjct: 76 RNVAMVFQDYALYPNMTVRGNLEFPLKMRRIGRAERRRRIEQVAGMLELMPLLDRRPAQL 135 Query: 149 SGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQ 208 SGGQ+QRVA+ RA+V P + LLDE L+ LD +LR Q++ ++ LQR+ G T ++VTHDQ Sbjct: 136 SGGQRQRVAMGRALVRDPSVFLLDEPLANLDARLRAQVRADIAELQRRTGTTMIYVTHDQ 195 Query: 209 EEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVIERLDEQRVR 268 EA+T+ RI V+ GR++Q +PRE+Y P N FVAGFIG M V + V Sbjct: 196 VEAMTLGQRIAVLAGGRLQQAASPRELYAHPANTFVAGFIGNPPMNLLPVRIGRSGETVL 255 Query: 269 ANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIGYVRERNYKG 324 + G A P +RPE +R+ E + +EG+ VRE Y G Sbjct: 256 PDFGGVP---LPGRADAPKDAAIAGIRPEAVRLAETS----SEGIAVRVREVEYLG 304 Lambda K H 0.319 0.136 0.385 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: 284 Number of extensions: 8 Number of successful extensions: 1 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: 378 Length of database: 356 Length adjustment: 30 Effective length of query: 348 Effective length of database: 326 Effective search space: 113448 Effective search space used: 113448 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 24 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