Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 332 bits (850), Expect = 1e-95 Identities = 172/349 (49%), Positives = 233/349 (66%), Gaps = 9/349 (2%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 G PV+ +++ I DGEFV+L+GPSGCGKST+LRM+AGLE+I+ G +RIG VVN LP + Sbjct: 14 GAFPVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEIRIGNQVVNRLPPK 73 Query: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 +R++AMVFQNYALYPHM+V DN+AF L RP +EID+RV A +L L LL+R PR Sbjct: 74 DRDIAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEILGLSKLLDRYPRQ 133 Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 +SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR +R +IK LHQRL+TTTVYVTHD Sbjct: 134 LSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELHQRLKTTTVYVTHD 193 Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Q+EAMT+AD++++M DG + Q G+P ELY P NLF AGFIG+PAMN L G + D + Sbjct: 194 QIEAMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPAMNMLKGRLDPADPSV 253 Query: 255 FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGA 314 F+ AL R + + +RP+++ + +P P + ++E G Sbjct: 254 FLTA--DGTALPVARPAAAAQGRDLVYGLRPEYMAL----DPNG---LPAEIAVIEPTGY 304 Query: 315 DALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESGENL 363 + L R G +T + +PG T+ LA+D +H+FD +G L Sbjct: 305 ETQLIARLGGHDVTCVFRERVNAKPGETIHLAIDAAHVHLFDAGTGRRL 353 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: 405 Number of extensions: 15 Number of successful extensions: 2 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: 355 Length adjustment: 30 Effective length of query: 376 Effective length of database: 325 Effective search space: 122200 Effective search space used: 122200 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