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 Ac3H11_794 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_794 Length = 270 Score = 140 bits (353), Expect = 3e-38 Identities = 80/264 (30%), Positives = 132/264 (50%), Gaps = 4/264 (1%) Query: 15 LLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQANFGRNLLN 74 L ++ +++++ P YW V SFK + + S SF P FT ++Y+ +F ++ +N Sbjct: 11 LFLIAYLLFALLPIYWMVNMSFKTNAEILSTF-SFFPQHFTWDNYKTIFTDESWYSGYIN 69 Query: 75 SLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQT 134 SLI +++L + + AAYA R F V + +L+ M P L F L Sbjct: 70 SLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTV 129 Query: 135 GLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTG 194 GL +TH+ + L +LLF++P VW+L G+ G+PRE++E AY+DG + + + + LPL Sbjct: 130 GLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIK 189 Query: 195 PGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVV 254 G+ F+ +W E L A T T SV P + + W ++ AA V+ Sbjct: 190 AGVGVAAFFCFMFSWVELLLARTLT---SVNAKPIVATMTRTVSASGMDWATLAAAGVLT 246 Query: 255 TVPLVVLVLVFQQRIVAGLTAGAV 278 VP +++ + I G G V Sbjct: 247 IVPGAIVIWFVRHYIAKGFAMGRV 270 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: 147 Number of extensions: 4 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: 270 Length adjustment: 25 Effective length of query: 255 Effective length of database: 245 Effective search space: 62475 Effective search space used: 62475 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