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 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 342 bits (878), Expect = 7e-99 Identities = 184/362 (50%), Positives = 249/362 (68%), Gaps = 12/362 (3%) Query: 1 MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60 MA V+L++V K +G+VV KD NL+ +GEFVVFVGPSGCGK+T LRMIAGLE I+ G++ Sbjct: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 Query: 61 YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120 +IG++ +ND PP +R + MVFQ+YALYPH++V ENM+FGL+L K+ I++RV + A + Sbjct: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120 Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180 L++ HLL+RKP+ LSGGQRQRVA+GR +V EP VFL+DEPLSNLDA LRV+MR EI++L Sbjct: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180 Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240 +RLG T IYVTHDQVEAMTL +IVV+ G + QV PL LY +PA+RFVAGFIGSP MN Sbjct: 181 KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN 240 Query: 241 FVRAGVEVQG-EKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPE 299 F+ V ++V + P + + + G + LG+RPEHL +P Sbjct: 241 FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL-------LPS 293 Query: 300 E--ENVLRGEVEVVEPLGAETEIHVAVNGTL--LVAKVDGHAPVKPGDKVELLADTQRLH 355 + + +L GEV+VVE LG ET+IH+ + LV + + V+ G + +R H Sbjct: 294 DIADVILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCH 353 Query: 356 AF 357 F Sbjct: 354 LF 355 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: 387 Number of extensions: 15 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: 371 Length adjustment: 30 Effective length of query: 346 Effective length of database: 341 Effective search space: 117986 Effective search space used: 117986 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