Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 229 bits (584), Expect = 1e-64 Identities = 116/249 (46%), Positives = 162/249 (65%), Gaps = 3/249 (1%) Query: 4 IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63 I + +AK + G VLH + L I GEF+ +LGPSGCGK+T+LR++AG E S G + + Sbjct: 8 IRLEHVAKEF-DGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIIL 66 Query: 64 GGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLN 123 G + D+P R V VFQ+YAL+PHMSV+DN+AFGLR P EI RV + ++ Sbjct: 67 DGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVG 126 Query: 124 LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQR 183 L R+P ++SGGQQQR AIARA++ P V L DEPLS LD KLR Q+R ++K+L + Sbjct: 127 LAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRRE 186 Query: 184 LRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL 243 + T ++VTHDQ EA +++DRV++M +G + Q G+P E+Y P N+F A F+G N Sbjct: 187 MGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVG--ETNVF 244 Query: 244 SGTVQRQDG 252 G + DG Sbjct: 245 EGVAGQSDG 253 Lambda K H 0.321 0.137 0.403 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: 361 Number of extensions: 9 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: 406 Length of database: 370 Length adjustment: 30 Effective length of query: 376 Effective length of database: 340 Effective search space: 127840 Effective search space used: 127840 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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