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 PfGW456L13_3040 Various polyols ABC transporter, permease component 2
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3040 Length = 276 Score = 163 bits (412), Expect = 4e-45 Identities = 92/275 (33%), Positives = 152/275 (55%), Gaps = 4/275 (1%) Query: 5 SRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFL 64 SR L L L + + FP +W V++SFK F+ P F+ +P TLE+Y ++ Sbjct: 6 SRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFMP-TLENYLHINE 64 Query: 65 QANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVL 124 ++++ NS++++ AT L L++ V AAY++ + +LS M P + VL Sbjct: 65 RSDYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTRGTLLWMLSTKMLPPVGVL 124 Query: 125 GGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQT 184 ++LL + GL +T + LI+ Y L LP VW++ YF+ +PR++ EAA +DGAT Q Sbjct: 125 MPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPRDILEAARLDGATLAQE 184 Query: 185 LLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPW 244 +L+V+LP+ GL +T LL+ I WNE ++L T S K P ++P + W Sbjct: 185 MLRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT---SSKAAPLTALIASYSSPEGLFW 241 Query: 245 GSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVK 279 + A S + P+++ + Q+++V GL+ GAVK Sbjct: 242 AKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 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: 135 Number of extensions: 8 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: 276 Length adjustment: 25 Effective length of query: 255 Effective length of database: 251 Effective search space: 64005 Effective search space used: 64005 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 Apr 09 2024. 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