Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate BPHYT_RS16105 BPHYT_RS16105 mannitol ABC transporter permease
Query= TCDB::O30493 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS16105 Length = 291 Score = 366 bits (939), Expect = e-106 Identities = 175/262 (66%), Positives = 216/262 (82%), Gaps = 2/262 (0%) Query: 15 GTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHINERSNYFSYAWN 74 G +AW +A+L+FFPIFWM +T+FKTE A+A+ F PTL+++ + RSNYFS+AWN Sbjct: 32 GVIAWLVALLLFFPIFWMTITAFKTEQQAYAS--SLFFIPTLDSFREVFARSNYFSFAWN 89 Query: 75 SVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAKSF 134 S+LIS T LCL+++VPAAY+MAF+ T+RT+ LLWMLSTKM+P VGVL+PIYLL K+ Sbjct: 90 SILISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNS 149 Query: 135 GLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAK 194 GLLD+ L+I+YTLINLPI VWM +TYF +IP+DILEA R+DGA WQE+V +L+P++ Sbjct: 150 GLLDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSL 209 Query: 195 GGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLFWAKLSAVSTLACAP 254 GLAST LL +IL WNEAFWS+NL+SSNAAPLT IASYSSPEGLFWAKLSA S LA AP Sbjct: 210 PGLASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAP 269 Query: 255 ILIFGWISQKQLVRGLSFGAVK 276 ILI GW+SQKQLVRGL+FGAVK Sbjct: 270 ILIVGWLSQKQLVRGLTFGAVK 291 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: 411 Number of extensions: 19 Number of successful extensions: 2 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: 291 Length adjustment: 26 Effective length of query: 250 Effective length of database: 265 Effective search space: 66250 Effective search space used: 66250 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