Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 230 bits (586), Expect = 3e-65 Identities = 122/245 (49%), Positives = 165/245 (67%), Gaps = 1/245 (0%) Query: 17 VSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQS 76 V + + I+ + K YG VL+ I+L V RGE I I G SGSGKST++RC+N LEE Q Sbjct: 18 VGEPPIVDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCVNGLEEFQE 77 Query: 77 GKIIVDGIELTSDLKN-IDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAE 135 G + V+G +L D + ++R +VGM+FQ FNLFPHL++ N+ LAP V+ + AE Sbjct: 78 GALSVNGKKLLHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAPTLVKARDAKTAE 137 Query: 136 ETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKE 195 A LE+V + E+ P QLSGGQQQRVAIAR+L M+P+++L DE TSALDPE++ E Sbjct: 138 TQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDEITSALDPELVGE 197 Query: 196 VLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQ 255 VL + LA+EGMT++ VTHEM FA+ V +RVIFM G++ EQ P F NPQ+ +Q Sbjct: 198 VLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGNPQTPELQQ 257 Query: 256 FLSQI 260 FLS + Sbjct: 258 FLSSL 262 Lambda K H 0.320 0.134 0.391 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: 195 Number of extensions: 5 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: 263 Length of database: 264 Length adjustment: 25 Effective length of query: 238 Effective length of database: 239 Effective search space: 56882 Effective search space used: 56882 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: 47 (22.7 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