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 AO353_25130 AO353_25130 ABC transporter
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 336 bits (861), Expect = 7e-97 Identities = 184/367 (50%), Positives = 245/367 (66%), Gaps = 21/367 (5%) Query: 1 MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60 M K++L++V K+ G V ++D +LE GEFVVFVGPSGCGK+T LR+IAGL+ I G++ Sbjct: 1 MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60 Query: 61 YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120 I +R VND+ P++R + MVFQ+YALYPHM+VY+N++FGL+L + K + RV A+I Sbjct: 61 LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120 Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180 L+++ LL RKP+ELSGGQRQRVAMGRA+ REP + L DEPLSNLDA LRV+MR EIA+L Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240 RLG T IYVTHDQVEAMTL +IVV+ G ++QV +P LY+ PA+RFVAGF+GSP MN Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPY------AGKEVWLGVRPEHLGLKGY 294 F+ A + GE + P VLG P+ A + LGVRPEH+ LK Sbjct: 241 FLAARLHAPGETSLVDTP--------VLGMTSLPFDSSNLAADTPLSLGVRPEHVSLKA- 291 Query: 295 TTIPEEENVLRGEVEVVEPLGAETEIHVAV-NGTLLVAKVDGHAPVKPGDKVELLADTQR 353 + + V VE LG+ET +H+ L+ + + +A + GD+VEL D Sbjct: 292 -----ADGTVGVIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGN 346 Query: 354 LHAFDLE 360 LH FD + Sbjct: 347 LHLFDAD 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: 420 Number of extensions: 19 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: 381 Length adjustment: 30 Effective length of query: 346 Effective length of database: 351 Effective search space: 121446 Effective search space used: 121446 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