Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 278 bits (710), Expect = 2e-79 Identities = 163/337 (48%), Positives = 215/337 (63%), Gaps = 16/337 (4%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MA L++ V K +G +VL +++L I GE ++ VGPSGCGKSTL+ IAGLE +T G + Sbjct: 1 MAALEINNVCKDFGSEQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSGEI 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 I G V PA+R IAMVFQSYALYP MTVR+N+SF L++ K +AE +AAVE A+ Sbjct: 61 RIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVADL 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 LQ+G L+R P LSGGQRQRVA+GR++ R+PKVYLFDEPLSNLDA LRV R EI +L Sbjct: 121 LQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKKLH 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + + +T+VYVTHDQ+EAMTLA I V+ G I Q+GSP E+Y P + FVA F+GSP M Sbjct: 181 QRL-GTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPSM 239 Query: 241 NLLPGKII-GTGAQTTVEMTDGGRAVS-------DYPSDDSLMGAAVNVGVRPEDMVE-A 291 N + ++ G+GA T G + + P+ +G V +G+RPE E Sbjct: 240 NFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTEDD 299 Query: 292 APGGDYVFEG-----KVAITEALGEVTLLYFEAPSGE 323 A G+Y EG ++ + E G LL + GE Sbjct: 300 ARLGEYA-EGVALTPRITVVEPTGADILLQLKLGDGE 335 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: 397 Number of extensions: 22 Number of successful extensions: 3 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: 373 Length of database: 373 Length adjustment: 30 Effective length of query: 343 Effective length of database: 343 Effective search space: 117649 Effective search space used: 117649 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: 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