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 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 190 bits (482), Expect = 6e-53 Identities = 113/302 (37%), Positives = 173/302 (57%), Gaps = 25/302 (8%) Query: 1 MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60 M+ + +E V + ++ +L GE +GPSGCGKTT L+ IAGL+ IS+G I Sbjct: 1 MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60 Query: 61 YIGDRLVND----VPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKE 116 I RL++ VP + R++ M+FQ+YAL+PH+ V EN+ FG++ K R+ E Sbjct: 61 SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARLGE 118 Query: 117 AARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEI 176 ++K+E L R P ELSGGQ+QRV++ RA+ EP++ L+DEP SN+DAK+R EM EI Sbjct: 119 MLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEI 178 Query: 177 AKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS 236 ++ ++ GV+ ++VTH + EA ++ + KDG I Q + +LY P +++VA F+G Sbjct: 179 REILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLG- 237 Query: 237 PSMNFVRAGVEVQGEKVYLVAPGFRIRANAVLG-----SALKPYAGKEVWLGVRPEHLGL 291 +N++ V+ R R +LG S L AG L +RPE L + Sbjct: 238 -QVNYLSCEVK------------DRARLQTLLGEVQSSSDLPKAAGYRGELLLRPEQLQM 284 Query: 292 KG 293 G Sbjct: 285 AG 286 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: 316 Number of extensions: 16 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: 376 Length of database: 342 Length adjustment: 29 Effective length of query: 347 Effective length of database: 313 Effective search space: 108611 Effective search space used: 108611 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: 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