Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3855 PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Phaeo:GFF3855 Length = 361 Score = 296 bits (759), Expect = 5e-85 Identities = 167/340 (49%), Positives = 217/340 (63%), Gaps = 9/340 (2%) Query: 19 VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78 VLH L+L I GEF+VLLG SGCGKST+L IAGL DIS G + I G V ER + Sbjct: 22 VLHQLNLDIEQGEFLVLLGSSGCGKSTLLNCIAGLLDISDGQIFIQGQNVTWAEPSERGI 81 Query: 79 AMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGG 138 MVFQ+YALYP M+V N++FGL+ + P AEI +RV A +L +E LL+RKP A+SGG Sbjct: 82 GMVFQSYALYPQMTVEGNLSFGLKNARLPKAEIAKRVARAAEVLQIEPLLKRKPAALSGG 141 Query: 139 QQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEA 198 Q+QR AI RA+++ VFLFDEPLSNLDAKLRA LR ++KRLHQ+L T +YVTHDQ+EA Sbjct: 142 QRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRADLRVELKRLHQQLANTMIYVTHDQVEA 201 Query: 199 MTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIET 258 MTLADR+ +M+ GRI+Q SP E+Y P+NL+ AGFIG+PAMN + G + DG + Sbjct: 202 MTLADRIAIMKGGRIMQLSSPDEIYNRPQNLYVAGFIGSPAMNLIEGVL--IDGVFHAGS 259 Query: 259 AHQRWALTGERFSRLR--HAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADA 316 AL +R+ H A + +RP+H+ + GE+ A T V V+LVE LG+D Sbjct: 260 L----ALPMQRYDYRNGPHHGAAVIGIRPEHI-LTGEQITRADATAEVLVDLVEGLGSDT 314 Query: 317 LLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 L+ G Q L + G L + D +FD Sbjct: 315 LVYATHGAQNLRLRMDGASRVSAGDRLRIGFDTGRASLFD 354 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: 393 Number of extensions: 17 Number of successful extensions: 3 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: 361 Length adjustment: 30 Effective length of query: 376 Effective length of database: 331 Effective search space: 124456 Effective search space used: 124456 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