Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_057508082.1 ABB28_RS07720 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc02869 (352 letters) >NCBI__GCF_001431535.1:WP_057508082.1 Length = 238 Score = 125 bits (313), Expect = 1e-33 Identities = 73/200 (36%), Positives = 109/200 (54%), Gaps = 11/200 (5%) Query: 20 LQLKTIRKAFGSHEV----LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75 L+++ + K F + +V L+ +DL V +GEFV GPSG GK+T L LE TSG+ Sbjct: 2 LEMRAVAKVFRTEQVETHALRSLDLLVNEGEFVAVTGPSGSGKTTFLNIAGLLETFTSGT 61 Query: 76 VQIDGVEVGHVAPAKRG------IAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEK 129 +DG +V + R I +FQ + L P L + DN+ + L+ G+ AE E+ Sbjct: 62 YLLDGQDVSTLGDDARSRLRNQKIGFIFQGFNLIPDLNLFDNVDVPLRYRGMSAAERRER 121 Query: 130 VAKAAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTR 189 + KA + L + P+ELSGGQ+QR AI RA+ P+L L DEP NLD+ + Sbjct: 122 IEKALSQVGLGSRMKHYPSELSGGQQQRAAIARALAGSPRLLLADEPTGNLDSTMARGV- 180 Query: 190 LEIARLHRSLKATMIYVTHD 209 +E+ + T++ VTHD Sbjct: 181 MELLEEINAAGTTIVMVTHD 200 Lambda K H 0.320 0.137 0.393 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: 177 Number of extensions: 8 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: 352 Length of database: 238 Length adjustment: 26 Effective length of query: 326 Effective length of database: 212 Effective search space: 69112 Effective search space used: 69112 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: 48 (23.1 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