Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 257 bits (657), Expect = 3e-73 Identities = 151/371 (40%), Positives = 214/371 (57%), Gaps = 47/371 (12%) Query: 1 MGQIQLTDLTKRFGD----TVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPT 56 M + L ++TKR+G + ++ ++ D EF+V+VGPSGCGKST LRM+AGLE + Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 SGDIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDE--- 113 G++ IG +N P RDIAMVFQ+YALYPHMT +N+ +GL+ +DE Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLK----IAKVPKDEIKA 116 Query: 114 RVVEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEM 173 RV + A+ L + LL+RKP ELSGGQ+QRVA+GRAIVR P+VFL DEPLSNLDAKLRA+ Sbjct: 117 RVDKAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQT 176 Query: 174 RTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAE 233 R E+Q L +L +T+++VTH+Q EAMT+A R+ VM+ G ++Q +P E YH P FVA Sbjct: 177 RLEIQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVAS 236 Query: 234 FIGEPMINLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDD 293 FIG P +NL++ + +LG+RPE ++V Sbjct: 237 FIGSPPMNLLKNAPGA----------------------QPGTILGIRPEHLDVR------ 268 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353 + V VE G + +++ + + + + V EG H + V Sbjct: 269 ----SEGWAVTVETVELLGAERLIY----GRINGEQVIVRVEEGTHSPEPDSVIHVQPRA 320 Query: 354 DKIHLFDAETG 364 D++H FDA TG Sbjct: 321 DRLHAFDAATG 331 Lambda K H 0.317 0.135 0.386 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: 339 Number of extensions: 16 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: 383 Length of database: 334 Length adjustment: 29 Effective length of query: 354 Effective length of database: 305 Effective search space: 107970 Effective search space used: 107970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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