Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 308 bits (789), Expect = 2e-88 Identities = 168/379 (44%), Positives = 233/379 (61%), Gaps = 22/379 (5%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + K Y G +H +DL I DGEF+V +GPSGC KST LRMIAGLEDISGG Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + IG VNDLP ++R +AMVFQNYALYPH +V+DN+AFGL+ KRP EI RRV + A Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 L + LL RKP+ MSGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR +R I +L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 181 HQRLR-----TTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235 H+ L+ T +YVTHDQ EA+TL DR+ ++ G I+Q +P +LY YP N F A FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 236 GTPAMNFLSGTVQRQDGQLFIETA--------HQRWALTGERFSRLRHAMAVKLAVRPDH 287 G+P++N + +++ + +L++E A H + L ++ V +RP+H Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINK-----PVCFGIRPEH 295 Query: 288 VRIAGEREPAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLP--QPGATLTL 345 + +A + + + ++V VE +G++ L G + L A V + G TL Sbjct: 296 ISLASDDDDLNTFEGVLTV--VENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRF 353 Query: 346 ALDQHELHVFDVESGENLS 364 L+ HVFD + NL+ Sbjct: 354 NLNTAFCHVFDFYNENNLT 372 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: 370 Number of extensions: 11 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: 376 Length adjustment: 31 Effective length of query: 375 Effective length of database: 345 Effective search space: 129375 Effective search space used: 129375 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