Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 201 bits (510), Expect = 3e-56 Identities = 130/301 (43%), Positives = 169/301 (56%), Gaps = 14/301 (4%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLE-KITGGTLEIDGTVVNDVPPAQRGI 77 L ++LDI GE +V +GPSGCGK+T LR+IAGLE GG + V +P QRG+ Sbjct: 23 LQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPIEQRGV 82 Query: 78 AMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGG 137 MVFQSYAL+P+MTV EN+++ L++ + A V+ + LG + +R LSGG Sbjct: 83 GMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQLSGG 142 Query: 138 QRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVE 197 QRQRVA+ R+I P+V L DEPL+ LDA LR A R +I QL ++ T VYVTHDQ E Sbjct: 143 QRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSL-HITAVYVTHDQAE 201 Query: 198 AMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVE 257 AM L RI+V+ G IAQ G+P ++Y P N FVA FIG+ MN LP + + Sbjct: 202 AMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLPAVLEADAWRVP-- 257 Query: 258 MTDGGRAVSDYPSDDSLMGA---AVNVGVRPEDMVEAAPGGDYVFEGKVAITEALGEVTL 314 G V + + SL A + RPED V A D G V LG T Sbjct: 258 ----GGLVPRHGTAASLAAAPSPRAELLFRPED-VALAQAEDAHLGGSVVTALFLGNYTR 312 Query: 315 L 315 L Sbjct: 313 L 313 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: 326 Number of extensions: 15 Number of successful extensions: 3 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: 357 Length adjustment: 30 Effective length of query: 343 Effective length of database: 327 Effective search space: 112161 Effective search space used: 112161 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 Sep 17 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