Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 219 bits (557), Expect = 1e-61 Identities = 124/311 (39%), Positives = 187/311 (60%), Gaps = 3/311 (0%) Query: 23 LDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVAMVF 82 + L+I GE LLG SG GKST+LRM+AG E + G + + G + D+P ER + M+F Sbjct: 39 VSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQDITDMPPYERPINMMF 98 Query: 83 QNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQR 142 Q+YAL+PHM+V NIAFGL++ K P AEI++RV+E+ L+++E +RKP +SGGQ+QR Sbjct: 99 QSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEPYAKRKPNQLSGGQRQR 158 Query: 143 AAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLA 202 A+AR++ K P + L DEP+ LD KLR Q++ ++ + + + T V VTHDQ EAMT+A Sbjct: 159 VALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGVTCVMVTHDQEEAMTMA 218 Query: 203 DRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETAH-Q 261 +R+ +M DG I Q GSP ++Y P N A FIG+ + F V+ + + I A+ Sbjct: 219 ERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGSVNL-FEGDIVEDEVDHVVINVANIP 277 Query: 262 RWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADALLTTR 321 + G S V +A+RP+ I+ E+ A C VE + LG ++ R Sbjct: 278 QPFYVGYGVSTSVDTTQVWVAIRPEKTHISREQPEDARNWCAGKVEDIAYLGGISVYYIR 337 Query: 322 -CGDQTLTALV 331 C Q + +++ Sbjct: 338 LCNGQLIQSVM 348 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: 287 Number of extensions: 6 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