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 RR42_RS18605 RR42_RS18605 sugar ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >FitnessBrowser__Cup4G11:RR42_RS18605 Length = 295 Score = 182 bits (463), Expect = 6e-51 Identities = 107/268 (39%), Positives = 158/268 (58%), Gaps = 10/268 (3%) Query: 16 LVVFVVVYSVFPFYWAVISSFKPSDALF--SPDPSFLPVPFTLEHYENVFLQANFGRNLL 73 L +FV V +FPFYW I++FKP L S +P ++ P T H++ + + LL Sbjct: 33 LGIFVFVL-LFPFYWMAITAFKPDGELLMRSANPFWVMAP-TFAHFKKLLFDTPYPEWLL 90 Query: 74 NSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQ 133 N++IV+ +T SL VLAAYA+ RL F V V + P + L ++ Q Sbjct: 91 NTVIVSTISTFASLAASVLAAYAIERLRFQGAKQVGLAVFLAYLIPPSILFIPLASIVFQ 150 Query: 134 TGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLT 193 GLF+T LILTY F +PF W+L+GYFR +P ELEE A +DGAT + L+K++LPL Sbjct: 151 LGLFDTRWALILTYPTFLIPFCTWLLMGYFRSIPYELEECALIDGATRWEILVKIILPLA 210 Query: 194 GPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIAS--FGGATPFEIPWGSIMAAS 251 PGL++ G+ AF +WNE+++ALTF VKTVP I + G WG++MA + Sbjct: 211 VPGLISAGIFAFTLSWNEFIYALTFISSSEVKTVPVGIVTELIEGDV---YHWGALMAGA 267 Query: 252 VVVTVPLVVLVLVFQQRIVAGLTAGAVK 279 ++ ++P+ ++ F + V+G+T GAVK Sbjct: 268 LLGSLPVALVYSFFVEYYVSGMT-GAVK 294 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: 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: 295 Length adjustment: 26 Effective length of query: 254 Effective length of database: 269 Effective search space: 68326 Effective search space used: 68326 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