Align Maltose transport system permease protein malG aka TT_C1629, 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_106712770.1 CU102_RS19475 carbohydrate ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >NCBI__GCF_003010955.1:WP_106712770.1 Length = 289 Score = 206 bits (525), Expect = 4e-58 Identities = 111/281 (39%), Positives = 159/281 (56%), Gaps = 4/281 (1%) Query: 2 RRASRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYEN 61 +R+ L RL YL ++ +V ++FP YW +SFK +F+ P +LP TL+HY+ Sbjct: 11 KRSRELFVRLSAYLTILVALVVTLFPVYWIAANSFKFDIDIFAVPPEWLPRHPTLKHYDE 70 Query: 62 VFLQANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPP--KNAVMYIVLSMTMFP 119 F+Q F R LNS +VA G T++S+ G +A YAL R +P + + + +LS M P Sbjct: 71 AFIQRPFLRYALNSFLVAMGTTVVSVGFGTMAGYALARFSYPWQWRKQISFWILSTRMMP 130 Query: 120 QIAVLGGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGA 179 I + L+L + NT LI+ Y F LPF W++ YF+ LP ELEEAA VDG Sbjct: 131 PIVSIIPLYLFFNYFDMLNTKSALIIAYTAFNLPFATWMMKSYFQDLPVELEEAAIVDGD 190 Query: 180 TPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATP 239 T L V LPL PGL T + I +WNE+L +L T+ + +T+P IA G T Sbjct: 191 TRWGAFLHVALPLARPGLAATAIFCLIISWNEFLLSLIITLTEQSQTLPIGIA--GRVTQ 248 Query: 240 FEIPWGSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280 ++ WG I AA + VP+V+ + Q+ +V GL+ GAVKG Sbjct: 249 YKTYWGEISAAGFMACVPIVIFAFIVQKHLVRGLSLGAVKG 289 Lambda K H 0.329 0.145 0.439 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: 146 Number of extensions: 5 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: 280 Length of database: 289 Length adjustment: 26 Effective length of query: 254 Effective length of database: 263 Effective search space: 66802 Effective search space used: 66802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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