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 Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 328 bits (841), Expect = 1e-94 Identities = 178/359 (49%), Positives = 235/359 (65%), Gaps = 21/359 (5%) Query: 11 KRFGK----VVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRL 66 KRFGK V ++ ++ GEF++ VGPSGCGK+T L +IAGL+E +EG I IG + Sbjct: 12 KRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKN 71 Query: 67 VNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHL 126 V +PP+DRDIAMVFQ+YALYP ++V +N+ F L +R+ PK E +R+ E A +L+I HL Sbjct: 72 VVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHL 131 Query: 127 LNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVT 186 L+R+P +LSGGQRQRVAMGRA+ R+P++FL DEPLSNLDAKLRVEMRAEI +L + G+T Sbjct: 132 LDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGIT 191 Query: 187 TIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGV 246 ++YVTHDQVEAMTLG RI VMK G +QQ+ TP +Y+ PAN +VA FIGSP+MN +R V Sbjct: 192 SVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAV 251 Query: 247 EVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRG 306 F I+ A L A P + EV LGVRPEHL + +E RG Sbjct: 252 ---------TGGQFGIQ-GAALNLAPPPSSANEVLLGVRPEHL-------VMQETAPWRG 294 Query: 307 EVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLETDRTI 365 V VVEP G +T + V + + D V+PG+ V L H FD +++ + Sbjct: 295 RVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353 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: 385 Number of extensions: 18 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: 355 Length adjustment: 30 Effective length of query: 346 Effective length of database: 325 Effective search space: 112450 Effective search space used: 112450 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