Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Burk376:H281DRAFT_05701 Length = 362 Score = 328 bits (842), Expect = 1e-94 Identities = 182/368 (49%), Positives = 237/368 (64%), Gaps = 10/368 (2%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + Q + K Y G VLH +D+ + DGEFVV++GPSGCGKST+LRM+AGLE IS GT Sbjct: 1 MAALTLQGVKKTYDGKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEGT 60 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + I G VVN+L ++RN+AMVFQNYALYPHMSV +N+ + L+ A+I +RV A Sbjct: 61 ISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAAQ 120 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L LE LL+RKPR +SGGQ+QR A+ RAI++ P+VFLFDEPLSNLDA+LR Q+R +I+RL Sbjct: 121 ILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H RL TT++YVTHDQ+EAMTLA RVI+M G Q G+P E+Y P +F AGFIG+P M Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPGM 240 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAV----KLAVRPDHVRIAGEREP 296 N L G V DG F + A L + + +A L +RP+H+ P Sbjct: 241 NLLEGRVS-DDGSTF-DVAGNGPQLPLAGVASIGREVAKGREWTLGIRPEHMSPGQADAP 298 Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 +LT V+ E+LGAD L R G +TA +P P G L +AL LH FD Sbjct: 299 HTTLT----VDSCELLGADNLAHGRWGKHDVTARLPHAHRPAAGEALQVALPARHLHFFD 354 Query: 357 VESGENLS 364 SG ++ Sbjct: 355 PASGRRVN 362 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: 426 Number of extensions: 16 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: 362 Length adjustment: 30 Effective length of query: 376 Effective length of database: 332 Effective search space: 124832 Effective search space used: 124832 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