Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 7025948 Shewana3_3096 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__ANA3:7025948 Length = 378 Score = 208 bits (530), Expect = 2e-58 Identities = 106/226 (46%), Positives = 152/226 (67%), Gaps = 2/226 (0%) Query: 23 LDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVAMVF 82 + L I GE LLG SG GKST+LRM+AG E + G + + G + DLP ER + M+F Sbjct: 39 VSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIFLDGEDITDLPPYERPINMMF 98 Query: 83 QNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQR 142 Q+YAL+PHM+V NIAFGL++ K P AEI++RV+E+ L+++E +RKP +SGGQ+QR Sbjct: 99 QSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQR 158 Query: 143 AAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLA 202 A+AR++ K P + L DEP+ LD KLR Q++ ++ + +R+ T V VTHDQ EAMT+A Sbjct: 159 VALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMA 218 Query: 203 DRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQ 248 R+ +M DG I Q GSP ++Y P + A FIG ++N G ++ Sbjct: 219 GRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIG--SVNLFGGEIE 262 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: 320 Number of extensions: 10 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