Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Ac3H11_2942 Various polyols ABC transporter, permease component 2
Query= TCDB::O30493 (276 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2942 Length = 279 Score = 353 bits (906), Expect = e-102 Identities = 172/276 (62%), Positives = 218/276 (78%), Gaps = 6/276 (2%) Query: 7 RRLQSLLLGTLA------WAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60 RR + LG LA W +A+L+FFP+ W+ LT+FKTE+ A A PP F+FTPTLEN+ Sbjct: 4 RRRSNFPLGLLALRTAAAWGVALLLFFPLGWLFLTAFKTELQAIAVPPLFVFTPTLENFH 63 Query: 61 HINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPP 120 + ERS+Y YA NSV+ S +T L L+++ PAAY+MAF++ K TK L+WMLSTKM+P Sbjct: 64 EVQERSDYLLYAKNSVITSVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPA 123 Query: 121 VGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGAT 180 VG L+PIY+LA+ LLDT++ALII++ L NLPI+VWM+Y++FKDIP +ILEAAR+DGAT Sbjct: 124 VGALVPIYVLAQKSHLLDTQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGAT 183 Query: 181 LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLF 240 LWQE+ VLLP+ GGLAST LL L+L WNEAFWSLNL+++ A L LIASYSSPEGLF Sbjct: 184 LWQEVRLVLLPLGMGGLASTGLLCLVLSWNEAFWSLNLSAAKAGTLATLIASYSSPEGLF 243 Query: 241 WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 WAKLSA S +A API++FGW SQKQLV+GL+FGAVK Sbjct: 244 WAKLSAASLMAIAPIVVFGWFSQKQLVQGLTFGAVK 279 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: 344 Number of extensions: 12 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: 279 Length adjustment: 25 Effective length of query: 251 Effective length of database: 254 Effective search space: 63754 Effective search space used: 63754 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