Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 308 bits (790), Expect = 1e-88 Identities = 168/365 (46%), Positives = 228/365 (62%), Gaps = 37/365 (10%) Query: 1 MADIHCQALAKHYAGGPP---VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDIS 57 MA + + + K Y GP V+H ++ + DGEFVV++GPSGCGKST+LRM+AGLE+IS Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 58 GGTLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVRE 117 GG LRIG VVNDL +R++AMVFQNYALYPHM+ ++N+A+GL+ K P EI RV + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 118 VAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDI 177 A +L L LLERKPR +SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLRAQ R +I Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 178 KRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGT 237 ++LH+ L T+++VTHDQ+EAMTLA R+I+M G + Q G+P E+Y P F A FIG+ Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 238 PAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPA 297 P MN L Q G + L +RP+H+ + E Sbjct: 241 PPMNLLKNAPGAQPGTI--------------------------LGIRPEHLDVRSEG--- 271 Query: 298 ASLTCPVSVELVEILGADALLTTRC-GDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 V+VE VE+LGA+ L+ R G+Q + + P+P + + + LH FD Sbjct: 272 ----WAVTVETVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFD 327 Query: 357 VESGE 361 +G+ Sbjct: 328 AATGK 332 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: 355 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 334 Length adjustment: 30 Effective length of query: 376 Effective length of database: 304 Effective search space: 114304 Effective search space used: 114304 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: 49 (23.5 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