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 HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 356 bits (914), Expect = e-103 Identities = 198/372 (53%), Positives = 252/372 (67%), Gaps = 21/372 (5%) Query: 1 MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60 MA V++ V K+FG ++ +++ DGEF V VGPSGCGK+T LRM+AGLEEI+ G I Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 61 YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120 IG +VN+V PKDRDIAMVFQNYALYPHM V +NMAF L L + K +D RVK+AA I Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180 L + LL+R PR+LSGGQRQRVAMGRAIVR+P+VFL DEPLSNLDAKLRV+MR EI +L Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240 +RL T+IYVTHDQ+EAMT+ +IVVM+DG ++Q PL+LYD+PAN FVAGFIGSP+MN Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240 Query: 241 FVRA-------GVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKG 293 F+ A G EV+ A G R+ A G+AL+ G++V GVRPEHL Sbjct: 241 FIPATLRRNATGAEVE------FADGTRV--PAPYGAALQGNDGQKVTYGVRPEHL---- 288 Query: 294 YTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQR 353 +I + +V VVEP GA+TE+ T L + GD + L+ D R Sbjct: 289 --SIGAAGQGIATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSR 346 Query: 354 LHAFDLETDRTI 365 H FD E+ +++ Sbjct: 347 THLFDAESGKSL 358 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: 409 Number of extensions: 17 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: 361 Length adjustment: 30 Effective length of query: 346 Effective length of database: 331 Effective search space: 114526 Effective search space used: 114526 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