Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 249 bits (635), Expect = 1e-70 Identities = 124/238 (52%), Positives = 168/238 (70%), Gaps = 1/238 (0%) Query: 16 GPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARE 75 G V+ LDL I +GEF+ LLGPSGCGK+T+LR+IAGLE + G + + + +PA Sbjct: 29 GKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPAEN 88 Query: 76 RNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAM 135 R V VFQ+YAL+PHM+V++N+AFGLR K PAAEI RV E ++ LE +RKP + Sbjct: 89 RYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQL 148 Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195 SGGQQQR AIARA++ P + L DE LS LD KLR Q++ ++K L ++L T V+VTHDQ Sbjct: 149 SGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQ 208 Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQ 253 EA+T++DR+++M+DGRI Q G+P E+Y P+NLF AGFIG M F + ++R D Q Sbjct: 209 EEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM-FNATVIERLDEQ 265 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: 349 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: 378 Length adjustment: 31 Effective length of query: 375 Effective length of database: 347 Effective search space: 130125 Effective search space used: 130125 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 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