Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Ac3H11_794 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= TCDB::O30493 (276 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_794 Length = 270 Score = 145 bits (367), Expect = 7e-40 Identities = 83/272 (30%), Positives = 138/272 (50%), Gaps = 8/272 (2%) Query: 7 RRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTP---TLENYLHIN 63 +R Q L +A+ + L+ PI+WMV SFKT + +T F F P T +NY I Sbjct: 4 KRFQKRTLFLIAYLLFALL--PIYWMVNMSFKTNAEILST---FSFFPQHFTWDNYKTIF 58 Query: 64 ERSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGV 123 +++S NS++ + L +++PAAY+ + Y K W+L+ +M PP Sbjct: 59 TDESWYSGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVF 118 Query: 124 LMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQ 183 L+P + L + GL+DT IA+ + + L ++P+ VW++ + IP++I E A +DG + + Sbjct: 119 LLPFFQLYTTVGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPR 178 Query: 184 EMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAK 243 + + LP+ K G+ + W E + LTS NA P+ A + S G+ WA Sbjct: 179 FFMTIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWAT 238 Query: 244 LSAVSTLACAPILIFGWISQKQLVRGLSFGAV 275 L+A L P I W + + +G + G V Sbjct: 239 LAAAGVLTIVPGAIVIWFVRHYIAKGFAMGRV 270 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: 259 Number of extensions: 14 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: 270 Length adjustment: 25 Effective length of query: 251 Effective length of database: 245 Effective search space: 61495 Effective search space used: 61495 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