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 Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 324 bits (830), Expect = 3e-93 Identities = 192/400 (48%), Positives = 252/400 (63%), Gaps = 43/400 (10%) Query: 1 MAKVRLEHVWKRF---------GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAG 51 +A V E + KRF G+VV + NLE DGEF+V VGPSGCGK+T LR++AG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LEEISEGNIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLR---------- 101 LE S G I +GDR V+ +P K RDIAMVFQ+YALYPH++VY+N+AFGLR Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 102 ------------LRRYPKDE--IDRRVKEAARILKIEHLLNRKPRELSGGQRQRVAMGRA 147 L+ P+ E I RRV+E A +L+++ LL+R+P++LSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 IVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVM 207 I R P+VFLMDEPLSNLDAKLR E RA+I LQR+LGVTT+YVTHDQ EAMT+G RI V+ Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 208 KDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKVYLVAPGFRIRANAV 267 G +QQV +PL +YD PANRFVA FIGSP MN + V + L FR Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRA---PLQLTTENFRCTLPEA 319 Query: 268 LGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVEPLGAETEI--HVAVN 325 L+ Y G+ V LG+RPEHL + + +N+L V VE LG++T I + + Sbjct: 320 WEPVLRLYDGQTVELGIRPEHLEVGAAAS----KNLLI-TVTGVEALGSDTFIAGELKES 374 Query: 326 GTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDLETDRTI 365 G + A++ + GD++ L ++H FDLET + I Sbjct: 375 GIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414 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: 479 Number of extensions: 17 Number of successful extensions: 4 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: 417 Length adjustment: 31 Effective length of query: 345 Effective length of database: 386 Effective search space: 133170 Effective search space used: 133170 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