Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 264 bits (675), Expect = 1e-75 Identities = 137/250 (54%), Positives = 173/250 (69%), Gaps = 11/250 (4%) Query: 12 PLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIM 71 P++DI LRK YG EVLKG+DL +QRG V+ +IG SGSGK+TLLRCVN LEEFQ G + Sbjct: 22 PIVDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCVNGLEEFQEGAL- 80 Query: 72 LDGESIGYDDIDGKRVRHPEKVIARH-RAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 130 ++GK++ H R R GM FQ FNLFPHL+ +N+ L VK Sbjct: 81 ---------SVNGKKLLHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAPTLVKAR 131 Query: 131 PKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 190 A A K LERVGL E+ D P QLSGGQQQRVAIARA+AM P ++L DE+TSALD Sbjct: 132 DAKTAETQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDEITSALD 191 Query: 191 PELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 250 PELVGEVL V++ LA++GMT+++VTHEM FA +V D+++FM+QGR+ EQG P LF PQ Sbjct: 192 PELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGNPQ 251 Query: 251 SPRLAEFLKN 260 +P L +FL + Sbjct: 252 TPELQQFLSS 261 Lambda K H 0.320 0.138 0.392 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: 204 Number of extensions: 7 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