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 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 333 bits (854), Expect = 4e-96 Identities = 184/364 (50%), Positives = 236/364 (64%), Gaps = 24/364 (6%) Query: 1 MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60 MA++RL HV KR+G V V+DF+L D EF+V +GPSGCGKTTT+RMIAGLEE S G I Sbjct: 1 MAEIRLNHVQKRWGSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEI 60 Query: 61 YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120 +IGDR+VN + PKDRD+AMVFQ+Y LYP+MNVYEN+ F L++R+ P+ E + RV A+ + Sbjct: 61 WIGDRMVNALDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARVMRASAM 120 Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180 ++++ L+RKP LSGGQRQRVA+ RAIVREP VFLMDEPLSNLDAKLRV RA+I L Sbjct: 121 VELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLS 180 Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240 L VTTIYVTHDQ+EAMTL R+VVM G +QQV TP+ +YD PAN FVA FIGSP+MN Sbjct: 181 HELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPAMN 240 Query: 241 FVRAGV---EVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTI 297 + V G++V + + L AG+ V LG R E + Sbjct: 241 LMEGAVTDGTFHGDRVAI--------------AGLSGAAGR-VTLGFRAED------AQV 279 Query: 298 PEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAF 357 + + + V +E LG T + V GTL+ K + G V++ T H F Sbjct: 280 VDSDGQIAAPVYSMELLGDATMVTVKAGGTLVAVKAPKEFRAEIGAPVQIRIPTGICHLF 339 Query: 358 DLET 361 D +T Sbjct: 340 DAQT 343 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: 12 Number of successful extensions: 2 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: 347 Length adjustment: 29 Effective length of query: 347 Effective length of database: 318 Effective search space: 110346 Effective search space used: 110346 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 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