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 N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 222 bits (565), Expect = 2e-62 Identities = 133/341 (39%), Positives = 201/341 (58%), Gaps = 30/341 (8%) Query: 6 LEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDR 65 + + +R+G A+ DF+L+ +GEFV +GPSG GK++ LR++AGL++ G++ Sbjct: 5 IRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGT 64 Query: 66 LVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLR----RYPKDEIDRRVKEAARIL 121 + +P + RDI +VFQ+YAL+PHM V +N+AFGLR+R R + +I RV++ R + Sbjct: 65 DLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRV 124 Query: 122 KIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQR 181 ++E L R P +LSGGQRQRVA+ RA+ EP + L+DEP LDA++R +R + LQR Sbjct: 125 QLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQR 184 Query: 182 RLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNF 241 LG+TT+ VTHDQ EA+ L R+VVM G I+QV P +Y PA FV GF+G N Sbjct: 185 SLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG--RANR 242 Query: 242 VRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHL-----GLKGYTT 296 +R VE ++++L F+ G AG+E+ +RPEHL GL G+T Sbjct: 243 IRGHVE--RDRLHLGGHSFQ-------GELPGDLAGREIEAWLRPEHLALASRGLGGWT- 292 Query: 297 IPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHA 337 G ++ ++ G +A++G LV + +A Sbjct: 293 ---------GRLQHLDLAGPVARARLAMHGDGLVLDAEWNA 324 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: 388 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: 384 Length adjustment: 30 Effective length of query: 346 Effective length of database: 354 Effective search space: 122484 Effective search space used: 122484 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: 50 (23.9 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