Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_110206230.1 DNK54_RS07055 ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >NCBI__GCF_003194585.1:WP_110206230.1 Length = 231 Score = 150 bits (378), Expect = 3e-41 Identities = 91/235 (38%), Positives = 140/235 (59%), Gaps = 18/235 (7%) Query: 12 PLLDIRGLRKQY----GPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 67 P+L+++G+RK Y G +E ++G+D + G V ++G SGSGK+TL+ + L+ Sbjct: 4 PVLELQGVRKTYSTGAGAVEAVRGIDAVVVAGEYVAVVGPSGSGKSTLMHILGCLDVPTS 63 Query: 68 GQIMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLK- 126 G+ ++ G+ + D + R+R + G FQQF+L P LTAL+NV L L+ Sbjct: 64 GRQLVRGQDVAAMD-------EAQLAAVRNREI-GFVFQQFHLLPGLTALRNVELPLIYA 115 Query: 127 -VKKLPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEV 185 V L + +A L RVGL +R DH PG+LSGGQQQRVAIARA+ +P+L+L DE Sbjct: 116 GVTALERRRRATVA---LTRVGLGDRADHRPGELSGGQQQRVAIARALVTDPALVLADEP 172 Query: 186 TSALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQG 240 T LD +VL + + L + G T++L+THE A E +D+++ + G +E+ G Sbjct: 173 TGNLDSRATADVLALFRELHDQGRTIVLITHEQEVAAE-ADRVLTLRDGLLEDAG 226 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: 130 Number of extensions: 5 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: 263 Length of database: 231 Length adjustment: 24 Effective length of query: 239 Effective length of database: 207 Effective search space: 49473 Effective search space used: 49473 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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