Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein
Query= TCDB::Q72L52 (376 letters) >NCBI__GCF_000769915.1:WP_035136158.1 Length = 234 Score = 136 bits (342), Expect = 7e-37 Identities = 79/219 (36%), Positives = 123/219 (56%), Gaps = 12/219 (5%) Query: 4 VRLEHVWKRFG----KVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59 +++E++ K F + A+ D ++E + GEFV +G SGCGK+T L ++ L+ S G+ Sbjct: 2 IKIENLSKVFRTEEVETKALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGGS 61 Query: 60 IYIGDRLVNDVPPKDR------DIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRR 113 + DR +N + ++ +I VFQN+ L ++VY+N+ L P E +R Sbjct: 62 YKLLDREINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIELPLIYNNVPSGERKKR 121 Query: 114 VKEAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMR 173 V+E A L I H L P++LSGGQ+QR A+ RA+V PK+ L DEP NLD+K E+ Sbjct: 122 VEEIAERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSKNGNEVM 181 Query: 174 AEIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEI 212 + L G T + VTH + +A + + + MKDG I Sbjct: 182 ELLTDLHAN-GATILMVTHSEYDA-SFSQKTIYMKDGMI 218 Lambda K H 0.320 0.139 0.400 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: 206 Number of extensions: 15 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: 376 Length of database: 234 Length adjustment: 26 Effective length of query: 350 Effective length of database: 208 Effective search space: 72800 Effective search space used: 72800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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