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 WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 140 bits (352), Expect = 4e-38 Identities = 84/266 (31%), Positives = 143/266 (53%), Gaps = 6/266 (2%) Query: 15 LLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQANFGRNLLN 74 LLV+ +V S+ P W V S P+ + P P T +Y +F + G N N Sbjct: 19 LLVLALV--SLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGVNFAN 76 Query: 75 SLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQT 134 SL+V+ TL SL+L +A YA +L F ++ + ++++ + P + LFLL++Q Sbjct: 77 SLLVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLMKQL 136 Query: 135 GLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLTG 194 GL N+ G+I+ L F ++++ Y R +P EL EAA +DGA ++ +++LP+ Sbjct: 137 GLVNSFGGVIVPALATV--FGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLPMLK 194 Query: 195 PGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVVV 254 P LVT + F+ AWN++++ L T+P A+A+ ++ +MA +VV Sbjct: 195 PVLVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVALATLSREHIMDVE--MMMAGAVVT 252 Query: 255 TVPLVVLVLVFQQRIVAGLTAGAVKG 280 +P++ L L+ Q+ + GL G+VKG Sbjct: 253 VIPVLALFLLLQRYYIQGLMLGSVKG 278 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: 137 Number of extensions: 3 Number of successful extensions: 1 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: 278 Length adjustment: 26 Effective length of query: 254 Effective length of database: 252 Effective search space: 64008 Effective search space used: 64008 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 24 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