Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_085635144.1 MGEO_RS02745 ATP-binding cassette domain-containing protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_002115805.1:WP_085635144.1 Length = 334 Score = 329 bits (843), Expect = 8e-95 Identities = 180/356 (50%), Positives = 234/356 (65%), Gaps = 28/356 (7%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 M ++L V K++GD++V+ ++L I+ GE VFVGPSGCGKSTLLR+IAGLE IT GT+ Sbjct: 1 MGRIQLKSVTKSFGDIQVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITTGTI 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 EIDG ++ PA+RG+AMVFQSYALYPHM+VR+N++F LK+AK AEID +EAAA Sbjct: 61 EIDGNDATNLVPAKRGLAMVFQSYALYPHMSVRKNIAFPLKMAKMDPAEIDKRIEAAASV 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 L L YLDR P LSGGQRQRVAIGR+IVR+P +LFDEPLSNLDAALRV RLEI++L Sbjct: 121 LNLTAYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + + +TM+YVTHDQVEAMT+A +IVVL G I QVGSPLELY++P N FVA FIGSPKM Sbjct: 181 KRLA-TTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPLELYQRPRNTFVAGFIGSPKM 239 Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300 NL+ G ++ A +G+RPE + + G ++ Sbjct: 240 NLISGA-------------------------EAQKHDAATIGIRPEHIDISESSG--AWK 272 Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKD 356 GK+ ++E LG T + + ++P + G G LT P +H F + Sbjct: 273 GKIGVSEHLGSDTFFHVQCDVTDEPLTVRATGEVSFKYGSEVYLTPRPEHLHRFNE 328 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: 378 Number of extensions: 23 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: 334 Length adjustment: 29 Effective length of query: 344 Effective length of database: 305 Effective search space: 104920 Effective search space used: 104920 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 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