Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 210 bits (534), Expect = 6e-59 Identities = 106/230 (46%), Positives = 147/230 (63%) Query: 7 QALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGT 66 + + K Y G ++ L+L I GEF+ LLGPSG GK+T L M+AG E + G + + G Sbjct: 14 RGIQKSYDGESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGR 73 Query: 67 VVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEA 126 +N++P +R++ MVFQNYAL+PHM+V +N+AF L +I RV+ A++ LE Sbjct: 74 AINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEG 133 Query: 127 LLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRT 186 R P +SGGQQQR A+ARA++ P + L DEPL LD +LR Q++ +IK LH+RL Sbjct: 134 FRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGV 193 Query: 187 TTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236 T VYVTHDQ EA+T++DRV + G+I Q P LY P N F A F+G Sbjct: 194 TVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLG 243 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: 353 Number of extensions: 14 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 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