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 GFF851 Psest_0865 ABC-type maltose transport systems, permease component
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__psRCH2:GFF851 Length = 296 Score = 112 bits (280), Expect = 1e-29 Identities = 86/282 (30%), Positives = 136/282 (48%), Gaps = 22/282 (7%) Query: 16 LVVFVVVYSVFPFYWAVISSFKPSD----ALFSPDPSF------LPVPFTLEHYENVFLQ 65 L+ FV +FP + SF+ + +LF +P+ L +P+T H + Q Sbjct: 20 LLAFVAAI-LFPLLMVISISFREGNFATGSLFPENPTLEHWSLALGIPYT--HADGSVTQ 76 Query: 66 ANFGRNLL--NSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAV 123 F L NS+ +A +++L L+L +AYA R+ F K ++ +L MFP + Sbjct: 77 PPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLS 136 Query: 124 LGGLFLLLRQTGLFNTHLGL-----ILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDG 178 L ++ L Q G + LG+ ++ L + +W + GYF + LEEAA VDG Sbjct: 137 LVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDG 196 Query: 179 ATPLQTLLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGAT 238 AT Q ++LP++ P L +LAFI + EY A + V + ++ + Sbjct: 197 ATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLM--DVDKLTLSVGAQQYLY 254 Query: 239 PFEIPWGSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVKG 280 P WG AA+V+ +P+ + L Q+ IV GLTAG VKG Sbjct: 255 PQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 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: 169 Number of extensions: 6 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: 280 Length of database: 296 Length adjustment: 26 Effective length of query: 254 Effective length of database: 270 Effective search space: 68580 Effective search space used: 68580 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 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