Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 143 bits (361), Expect = 5e-39 Identities = 80/217 (36%), Positives = 123/217 (56%), Gaps = 4/217 (1%) Query: 2 ATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGA 61 + V + S SY P + NL I G+ ++G SGCGKST L+M+AGL +DG Sbjct: 6 SNVWIAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGV 65 Query: 62 IFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAA 121 + I K V + + M+FQ +LYP M+V EN L AG + + RV+E Sbjct: 66 VRINGKTVVKPSAKWN---MMFQKPSLYPWMSVRENAALGLVFAGTYKQK-QDRVEELLD 121 Query: 122 TLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAAL 181 +GL+E ++ + LSGGQ+QRVA+ R++ P++ L+DEP S LDA R +T++A + Sbjct: 122 MVGLSEHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQI 181 Query: 182 QRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVG 218 + G+T + VTHD EA+ M D++ ++ + VG Sbjct: 182 CHEQGITMIMVTHDIEEAIAMADKVVIMSHNPGEIVG 218 Lambda K H 0.316 0.135 0.380 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: 205 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 376 Length of database: 263 Length adjustment: 27 Effective length of query: 349 Effective length of database: 236 Effective search space: 82364 Effective search space used: 82364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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