Align MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease
Query= TCDB::O30492 (296 letters) >FitnessBrowser__Phaeo:GFF726 Length = 315 Score = 114 bits (285), Expect = 3e-30 Identities = 83/274 (30%), Positives = 139/274 (50%), Gaps = 10/274 (3%) Query: 6 KNRLANPGWFLVTPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENQFVGLENFTYFITD 65 +NR A W + P V L ++I P+ + S R++ L G+ QF+G+EN+ + D Sbjct: 26 RNRQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWDGL--GDPQFIGMENYRELMDD 83 Query: 66 SGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVLLISPFFIMPTVGAL 125 F N L + + L+++ G+ I+ L + G + + L PF I V L Sbjct: 84 RAFEVSLWNNLKWL-LLYLLAIPAGLFIALFLNQT-VTGIRLYKSLFFFPFVISQVVVGL 141 Query: 126 IWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLLSIIIIVS--WQWLPFAILLLMTAMQ 183 ++ + + P G+L V + G P++ L L++ II++ W + ++L +T + Sbjct: 142 VF-SWFYDPTFGLLNQVLAWVGLGPINVLGDPTLVTYGIIIAGLWPQTAYCMILYLTGLN 200 Query: 184 SLDQEQKEAARLDGAGAIAIFWHLTLPHLARPIAVVVMIETIF-LLSVFAEIFTTTNGGP 242 ++D EQ EAARLDGA + W++ +P L RP V + TI L F I TNGGP Sbjct: 201 AVDPEQVEAARLDGAKGAKMLWYVIIPQL-RPATFVAFVVTIIGALRSFDLISIMTNGGP 259 Query: 243 GYASTNLAYLIYNQALVQFDVGMASAGGLIAVVI 276 +S L++ ++ +AL ++ M G IAVV+ Sbjct: 260 FGSSRVLSFYMFEKALSEYGFRM-GYGAAIAVVL 292 Lambda K H 0.328 0.143 0.437 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: 249 Number of extensions: 17 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: 296 Length of database: 315 Length adjustment: 27 Effective length of query: 269 Effective length of database: 288 Effective search space: 77472 Effective search space used: 77472 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: 48 (23.1 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