Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_002899945.2:WP_103234822.1 Length = 416 Score = 146 bits (369), Expect = 8e-40 Identities = 77/233 (33%), Positives = 133/233 (57%), Gaps = 1/233 (0%) Query: 14 KKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYF-DDRLVASN 72 K G + ++ + I GE F I+G SG+GK+T +R + L+ P++G++Y DD + + N Sbjct: 44 KTGCTIGINKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKN 103 Query: 73 GKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHH 132 K ++ ++ MVFQ + L P+ T +N F L K ++ ++ I+ ++ Sbjct: 104 NKELLEVRRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNG 163 Query: 133 VLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGV 192 N +P +LSGG QQRV LARAL DP +LL+DE FS LD ++ + + E+Q+ L Sbjct: 164 FENQYPSQLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQK 223 Query: 193 TLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245 T++ ++HD + I DR+ ++ G + Q+G ED+ NP S V + + +++ Sbjct: 224 TIVFITHDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVD 276 Lambda K H 0.319 0.139 0.390 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: 322 Number of extensions: 14 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: 353 Length of database: 416 Length adjustment: 30 Effective length of query: 323 Effective length of database: 386 Effective search space: 124678 Effective search space used: 124678 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 (21.7 bits) S2: 50 (23.9 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