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 BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 362 bits (928), Expect = e-104 Identities = 198/374 (52%), Positives = 251/374 (67%), Gaps = 12/374 (3%) Query: 1 MAKVRLEHVWKRFGK-VVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59 MA V L + KR+ AV +LE DGEF+VFVGPSGC K+TTLRMIAGLE+IS G Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 IYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR 119 IYIG+R VND+PPKDR IAMVFQNYALYPH V++NMAFGL++++ PKDEI RRV++AA Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179 L+I LL RKP+E+SGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRV MR +IA+L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 QRRL-----GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFI 234 R L T IYVTHDQ EA+TLG RI V+ G I QVDTP +LY++P N+FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 235 GSPSMNFVRAGVEVQGEKVYL-VAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKG 293 GSPS+N + + E++Y+ +APG I L+ Y K V G+RPEH+ L Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISL-- 298 Query: 294 YTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGH--APVKPGDKVELLADT 351 + ++ N G + VVE +G+E ++ V G L+A+VD P G + +T Sbjct: 299 -ASDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRFNLNT 357 Query: 352 QRLHAFDLETDRTI 365 H FD + + Sbjct: 358 AFCHVFDFYNENNL 371 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: 433 Number of extensions: 15 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: 376 Length adjustment: 30 Effective length of query: 346 Effective length of database: 346 Effective search space: 119716 Effective search space used: 119716 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