Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate GFF1916 PGA1_c19480 ABC transporter, inner-membrane protein
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__Phaeo:GFF1916 Length = 297 Score = 374 bits (959), Expect = e-108 Identities = 175/288 (60%), Positives = 229/288 (79%), Gaps = 1/288 (0%) Query: 18 GRKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEP 77 G KP R S R I +Y L V A ++L+P+Y++IVTSLK MPEIR+GN+ P + + Sbjct: 11 GPKPTRR-SMRRIAIYVFLSVAAAFFLMPIYIVIVTSLKTMPEIRLGNVLQWPQTWSVDA 69 Query: 78 WVKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTI 137 W+KAW ACTGL C+G+ GFWNS+RI +PS+++SI ++ GY L W F+GA++FF I Sbjct: 70 WIKAWDTACTGLQCEGIKVGFWNSMRILLPSLVVSITAGALCGYILTFWTFRGAEIFFAI 129 Query: 138 LIVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELF 197 L+ GAF+PYQ +I+P++ + G+YGTL G+++VHTIFG+PI+TL+FRNY++ LP E+F Sbjct: 130 LLFGAFVPYQALIFPMIRIFSATGLYGTLPGIVLVHTIFGLPIMTLIFRNYYSTLPSEIF 189 Query: 198 KAARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLN 257 KAARVDGAGF+++++ ++LP+S PI VVA ILQVTGIWND+L G++F E PMTVQLN Sbjct: 190 KAARVDGAGFFSVFWYVLLPISTPIIVVAAILQVTGIWNDYLLGLIFGGRENMPMTVQLN 249 Query: 258 NIVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 NIVNSV+G KEYNVNMAAT+LT LVPLTVYFVSGR FVRGIAAGAVKG Sbjct: 250 NIVNSVRGGKEYNVNMAATLLTALVPLTVYFVSGRWFVRGIAAGAVKG 297 Lambda K H 0.329 0.145 0.450 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: 364 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: 305 Length of database: 297 Length adjustment: 27 Effective length of query: 278 Effective length of database: 270 Effective search space: 75060 Effective search space used: 75060 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 (21.8 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