Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_011840778.1 RSPH17029_RS05420 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_000015985.1:WP_011840778.1 Length = 354 Score = 282 bits (722), Expect = 9e-81 Identities = 173/329 (52%), Positives = 205/329 (62%), Gaps = 20/329 (6%) Query: 18 VQLAGIRKCFDGKEV----IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGR 73 V+ + K F EV + + + I GEF TLLGPSGCGKTT+LRLIAG E SG Sbjct: 7 VEARHVVKAFGQGEVAVRALDDVSVGIRRGEFFTLLGPSGCGKTTLLRLIAGFEAPTSGA 66 Query: 74 IMLDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALR 133 I+LD DIT +P R +NTVFQSYALFPH+TV ENV FGLRMQ P AEI L Sbjct: 67 ILLDGRDITALPPNRRPINTVFQSYALFPHLTVAENVGFGLRMQGKPRAEIETVTARMLA 126 Query: 134 MVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKAL 193 +V+LE AQRK QLSGGQQQRVA+ARA+ +PR+LLLDE LSALD KLRK+MQ ELK L Sbjct: 127 LVRLEALAQRKVAQLSGGQQQRVALARALAPQPRVLLLDEPLSALDLKLRKEMQIELKRL 186 Query: 194 QRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM 253 Q + GITFVFVTHDQEEALTMSDRI VM GRI Q G PREIY P N FVA FIGE N Sbjct: 187 QHETGITFVFVTHDQEEALTMSDRIGVMSAGRILQIGPPREIYTRPANRFVASFIGETNF 246 Query: 254 FNATVIERLDEQRVRANVEGRECNIYVNFAVE--PGQKLHVLLRPEDLRVEEINDDNHAE 311 A R RV + G A+E P ++ V +RPE +R+ ++ Sbjct: 247 LPA----RHAGGRVTLDAGG-------ELAIEGGPEGRVTVAVRPEQVRLVAPDEPG--- 292 Query: 312 GLIGYVRERNYKGMTLESVVELENGKMVM 340 L +R+ Y G + L +G V+ Sbjct: 293 ALPATIRDLVYFGTDTHCHLALADGTEVV 321 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: 346 Number of extensions: 11 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: 354 Length adjustment: 30 Effective length of query: 348 Effective length of database: 324 Effective search space: 112752 Effective search space used: 112752 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 Apr 10 2024. 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