Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 217 bits (553), Expect = 4e-61 Identities = 121/287 (42%), Positives = 179/287 (62%), Gaps = 13/287 (4%) Query: 9 LAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVV 68 ++K +A VL +L I DGEF +LGPSGCGK+T+LR+IAG E + G + + G + Sbjct: 12 ISKRFAS-QEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDI 70 Query: 69 NDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALL 128 +PA +R VFQ+YAL+PH++V+DN+AFGL+ +I RV + A++ L Sbjct: 71 ARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFA 130 Query: 129 ERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTT 188 RKP +SGGQ+QR AIARA++ P + L DE LS LD KLR Q++ ++K+L ++L T Sbjct: 131 TRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITF 190 Query: 189 VYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQ 248 VYVTHDQ EA++++DR+++M +G+ Q G+P E+Y PRNLF A FIG +N G + Sbjct: 191 VYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG--EINVFDGEIV 248 Query: 249 RQDGQLFIETAHQRWALTG-ERFSRLRHAMA----VKLAVRPDHVRI 290 + G+ E ++ G R R H A V + +RP+ +RI Sbjct: 249 QALGEYQYEA-----SINGVVREIRCDHRFAVGDKVHVMLRPEDLRI 290 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: 329 Number of extensions: 13 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: 369 Length adjustment: 30 Effective length of query: 376 Effective length of database: 339 Effective search space: 127464 Effective search space used: 127464 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