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 HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__HerbieS:HSERO_RS16730 Length = 293 Score = 184 bits (466), Expect = 3e-51 Identities = 104/265 (39%), Positives = 158/265 (59%), Gaps = 4/265 (1%) Query: 16 LVVFVVVYSVFPFYWAVISSFKPSDALFSPDPS-FLPVPFTLEHYENVFLQANFGRNLLN 74 L++F+ V +FPFYW VI++FKP + L S + F + TL H++ + + LLN Sbjct: 31 LLIFLFVL-LFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLLFDTQYPAWLLN 89 Query: 75 SLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQT 134 ++IV+ +T SL V AAYA+ RL F V + + P + L ++ + Sbjct: 90 TVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIFLAYLIPPSILFIPLAAIVFKL 149 Query: 135 GLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTG 194 GLF+T LILTY F +PF W+L+GYFR +P ELEE A +DGAT + L+K++LPL Sbjct: 150 GLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIILPLAV 209 Query: 195 PGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVV 254 PGL++ G+ AF +WNE+++ALTF VKTVP I + WG++MA +++ Sbjct: 210 PGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVT-ELVEGDVYHWGALMAGALLG 268 Query: 255 TVPLVVLVLVFQQRIVAGLTAGAVK 279 ++P+ V+ F + V+G+T GAVK Sbjct: 269 SLPVAVVYSFFVEYYVSGMT-GAVK 292 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: 178 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 280 Length of database: 293 Length adjustment: 26 Effective length of query: 254 Effective length of database: 267 Effective search space: 67818 Effective search space used: 67818 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