Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_084058299.1 B9A12_RS12455 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_900176285.1:WP_084058299.1 Length = 367 Score = 160 bits (406), Expect = 4e-44 Identities = 113/358 (31%), Positives = 176/358 (49%), Gaps = 9/358 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 L L V++ L ++ L+ G + +G + GK+TLLR++AGL++ T G + +D Sbjct: 3 LTLEHVDRIVDGETHLCDVTLEFPSGSRNILLGRTLAGKTTLLRIMAGLDRPTRGRVLVD 62 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 G V V +R +AMV+Q + YP TV +N++ L++ + EID V AE L+L Sbjct: 63 GKDVTGVSVRKRNVAMVYQQFINYPSFTVYDNIASPLRLQGVPREEIDRRVREVAEMLRL 122 Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 LDRLP LSGGQ+QR AI R++V+D + L DEPL NLD LR R E+ + E Sbjct: 123 TPLLDRLPAQLSGGQQQRTAIARALVKDADLLLLDEPLVNLDYKLREELREELTAIFE-R 181 Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 S +VY T + EA+ L +V+L G + Q G ++Y +P A+ P +N L Sbjct: 182 GRSIVVYTTTEPTEALMLGGNVVILDEGRVLQTGPTDQVYHRPTTMRAAEVYSDPPINYL 241 Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPED-MVEAAPGGDYVFEGK 302 + G+ A+ ++T A + L + G+R ++ D E + Sbjct: 242 DLVVEGSQARIGEQVTFALCA-----HLEGLAPGRYHAGLRANRFFLKRRTDRDVALESQ 296 Query: 303 VAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKDGVSL 360 V ++E G T ++ P + GI G + A+PA+ VF SL Sbjct: 297 VELSEINGSETFIHVNHQG--FPLVVHETGIRTYKMGSTVTVHADPAQFFVFNQEGSL 352 Lambda K H 0.316 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: 325 Number of extensions: 11 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: 373 Length of database: 367 Length adjustment: 30 Effective length of query: 343 Effective length of database: 337 Effective search space: 115591 Effective search space used: 115591 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: 49 (23.5 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