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 WP_008410843.1 DESHY_RS13325 ABC transporter ATP-binding protein
Query= TCDB::Q72L52 (376 letters) >NCBI__GCF_000315365.1:WP_008410843.1 Length = 363 Score = 145 bits (365), Expect = 2e-39 Identities = 112/351 (31%), Positives = 181/351 (51%), Gaps = 22/351 (6%) Query: 23 NLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK-DRDIAMVF 81 N GE + +GP+G GK++ ++++A LE+ +G I R V P + R +AMVF Sbjct: 27 NFVLHKGETIALIGPNGAGKSSLVKLLALLEKPWQGEIIFDGRQVTGSPLQVRRQMAMVF 86 Query: 82 QNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHLLNRKPRELSGGQRQR 141 Q AL +V+ N+A GLR R P+D+I RRV + L+I HL +R R LSGG+ QR Sbjct: 87 QE-ALLLSGSVFGNVAQGLRFRGLPRDQIARRVNYWLKKLQIAHLADRHIRYLSGGEAQR 145 Query: 142 VAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHDQVEAMTLG 201 V++ RA+ EP+V +DEP + LD R+ + EI ++ + T+++TH+ E L Sbjct: 146 VSIARALALEPQVLFLDEPFAALDLPTRITLIEEIGEIIKATATATVFITHNVEEIPLLA 205 Query: 202 HRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKVYLVAPGFR 261 R+ M G+I Q + +++ +P N VA +G ++ +QG +V PG R Sbjct: 206 GRVCAMSAGKIVQDCSTEDIFRYPVNEEVARLVGIENV--------LQG----VVLPGGR 253 Query: 262 ---IRANAVLGSALKPY-AGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVEPLGAE 317 + + A + Y G + L +RPE + L N+ RG V + PL ++ Sbjct: 254 TAQVGETVISFVARQDYRPGTNINLCIRPEDVILIEDRKPDGGPNLCRGRVTKIYPLSSQ 313 Query: 318 TEIHV--AVNGTLLVAKVDGHA-PVKPGDKVELLADTQRLHAFDLETDRTI 365 ++ V + TL V K A V+ G V ++ ++++ L TDR I Sbjct: 314 LKLTVDCGFSITLQVNKELFFAGRVRSGSLVNIMLPPEKIYGLPL-TDRGI 363 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: 291 Number of extensions: 16 Number of successful extensions: 1 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: 363 Length adjustment: 30 Effective length of query: 346 Effective length of database: 333 Effective search space: 115218 Effective search space used: 115218 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 24 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