Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease
Query= TCDB::O30493 (276 letters) >NCBI__GCF_000621325.1:WP_084260334.1 Length = 281 Score = 358 bits (918), Expect = e-104 Identities = 173/260 (66%), Positives = 214/260 (82%) Query: 17 LAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINERSNYFSYAWNSV 76 LAWAI +IFFP+ +M +T+FKTE+ A A P ++FTPT EN+ + ERS YF YAWNSV Sbjct: 22 LAWAITFIIFFPLLFMFVTAFKTELQAIAVPSVWVFTPTWENFALVQERSGYFDYAWNSV 81 Query: 77 LISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAKSFGL 136 + S +T L LLI+VPAAYSMAF TKRTK L+WMLSTKM+P VG L+PIY+L ++FGL Sbjct: 82 ITSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVLCQTFGL 141 Query: 137 LDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAKGG 196 LD I+LIII+T++NLPI+VWM+Y+ FKDIP +ILEAAR+DGA+L +E VLLP+A GG Sbjct: 142 LDNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLLPLAMGG 201 Query: 197 LASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKLSAVSTLACAPIL 256 +AST LL L+L WNEAFW LNLT++NA L +L+ASYSSPEGLFWAKLSAVS LA API+ Sbjct: 202 MASTGLLCLVLSWNEAFWVLNLTAANAGTLASLVASYSSPEGLFWAKLSAVSVLAIAPIV 261 Query: 257 IFGWISQKQLVRGLSFGAVK 276 +FGW SQKQLV+GL+FGAVK Sbjct: 262 VFGWFSQKQLVQGLTFGAVK 281 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: 386 Number of extensions: 13 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: 276 Length of database: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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 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