Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 203 bits (517), Expect = 5e-57 Identities = 126/357 (35%), Positives = 201/357 (56%), Gaps = 36/357 (10%) Query: 1 MVRIIVKNVSKVFKKGKVV--ALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPS 58 M + ++N++K + G + VN +++GE I+GPSG GK+T +R++AGL+ S Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 TGELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIR 118 GEL DR+V + P R I MVFQ +ALYP++T FEN+A+ L K+ K+EI+ Sbjct: 61 GGELRIGDRVVND-----LEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIK 115 Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178 RV++ AKIL++ H+L PRELSGGQ+QRVA+ RA+V+ P + L DEP SNLDA++R Sbjct: 116 ARVDKAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQ 175 Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238 R ++++ LG+T L V+HD + +A R+ V+ G + Q G PE++Y P + VA Sbjct: 176 TRLEIQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVA 235 Query: 239 SLIGE--INELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILV 296 S IG +N L+ G G+ I+GIRPE + ++ + W + Sbjct: 236 SFIGSPPMNLLKNA---PGAQPGT------------ILGIRPEHLD-----VRSEGWAVT 275 Query: 297 GKGKVKVIGYQGGLFRITITPLDSEEEIFTYSD--HPIHSGEEVLVYVRKDKIKVFE 351 + V+++G + R+ ++ E+ I + H + V R D++ F+ Sbjct: 276 VE-TVELLGAE----RLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAFD 327 Lambda K H 0.319 0.139 0.390 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: 298 Number of extensions: 18 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: 353 Length of database: 334 Length adjustment: 29 Effective length of query: 324 Effective length of database: 305 Effective search space: 98820 Effective search space used: 98820 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 (21.7 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