Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 281 bits (718), Expect = 3e-80 Identities = 162/362 (44%), Positives = 221/362 (61%), Gaps = 14/362 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + Q + K + G V ++L I +GEFVV +GPSGCGKST+LRMIAGLE I+ G Sbjct: 1 MASVQLQNVTKAW-GEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L IG +ND P ER V MVFQ+YALYPH+SV +N++FGL+ I++RV +VA Sbjct: 60 LFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAE 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L LL+RKP+A+SGGQ+QR AI R ++ PSVFL DEPLSNLDA LR Q+R +I RL Sbjct: 120 VLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+RL T +YVTHDQ+EAMTLAD+++++ GR+ Q G P ELY YP + F AGFIG+P M Sbjct: 180 HKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKM 239 Query: 241 NFL-----SGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGERE 295 NFL + + + +L + Q W R ++ M+ L +RP+H+ Sbjct: 240 NFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMS--LGIRPEHLL----PS 293 Query: 296 PAASLTCPVSVELVEILGADALLTTRCGD--QTLTALVPADRLPQPGATLTLALDQHELH 353 A + V++VE LG + + + Q L L + GAT + L H Sbjct: 294 DIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCH 353 Query: 354 VF 355 +F Sbjct: 354 LF 355 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: 375 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 376 Effective length of database: 341 Effective search space: 128216 Effective search space used: 128216 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