Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_001294205.1:WP_053938866.1 Length = 242 Score = 227 bits (579), Expect = 2e-64 Identities = 119/246 (48%), Positives = 166/246 (67%), Gaps = 10/246 (4%) Query: 15 LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74 ++ I+++ K YG +VL +++G VV + G SGSGK+TL++CVN LE FQ G I++ Sbjct: 1 MISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIV 60 Query: 75 DGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134 DG S+G + N + + R+ GM FQ F LFPHL+ QN+TL ++V ++ Sbjct: 61 DGTSVGDPKTN----------LPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRNR 110 Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194 DEA V + L+RVGL D +PGQLSGGQQQRVAIARA+AM+P MLFDE TSALDPE Sbjct: 111 DEATVNGLRLLDRVGLKAHADKHPGQLSGGQQQRVAIARALAMDPIAMLFDEPTSALDPE 170 Query: 195 LVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254 +V EVL V+ LA++GMTM+ VTHEM FA +V+++++FM++G I E ++ F P+S Sbjct: 171 MVNEVLDVMVELAQEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFGSPRSE 230 Query: 255 RLAEFL 260 R FL Sbjct: 231 RAQVFL 236 Lambda K H 0.319 0.135 0.379 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: 163 Number of extensions: 4 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: 265 Length of database: 242 Length adjustment: 24 Effective length of query: 241 Effective length of database: 218 Effective search space: 52538 Effective search space used: 52538 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