Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF851 Psest_0865 ABC-type maltose transport systems, permease component
Query= TCDB::O30493 (276 letters) >FitnessBrowser__psRCH2:GFF851 Length = 296 Score = 102 bits (253), Expect = 1e-26 Identities = 87/288 (30%), Positives = 131/288 (45%), Gaps = 23/288 (7%) Query: 8 RLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLEN--------Y 59 RL + LA+ AIL FP+ ++ SF+ FAT F PTLE+ Y Sbjct: 12 RLWATHAALLAFVAAIL--FPLLMVISISFRE--GNFATGSLFPENPTLEHWSLALGIPY 67 Query: 60 LHINERSNY-----FSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLS 114 H + + WNSV I+F ++ L LL+S +AY+ A L ML Sbjct: 68 THADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLI 127 Query: 115 TKMLPPVGVLMPIYLLAKSFGLLDTRIAL-----IIIYTLINLPIVVWMVYTYFKDIPKD 169 +M PPV L+ IY L G + + + +I+ +L + + +W + YF+ I Sbjct: 128 FQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDAS 187 Query: 170 ILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNE-AFWSLNLTSSNAAPLTA 228 + EAA +DGAT WQ +LLP++ LA +L+ I E S+ L + L+ Sbjct: 188 LEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSV 247 Query: 229 LIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 Y P+ W +A + L+ PI QK +V GL+ G VK Sbjct: 248 GAQQYLYPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 Lambda K H 0.327 0.137 0.426 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: 263 Number of extensions: 19 Number of successful extensions: 4 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 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 (21.7 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