Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate GFF3012 HP15_2956 sugar ABC transporter, permease protein
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__Marino:GFF3012 Length = 289 Score = 326 bits (835), Expect = 5e-94 Identities = 146/276 (52%), Positives = 208/276 (75%) Query: 30 IIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWVKAWAEACTGL 89 + +YG L++ AL YL+PL++M+VTS K +IR GN+ A P + T W KAW+EACTG+ Sbjct: 14 VAIYGLLLLAALVYLIPLFIMLVTSFKTPMDIRTGNLMALPTDWTTIGWTKAWSEACTGV 73 Query: 90 NCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQVM 149 C+G+S FWNS ++TVP+V+IS + + NGY L+ W+FKG+DLFF +L+ G F+P+QV+ Sbjct: 74 QCEGISGYFWNSFKMTVPAVLISTLLGAFNGYVLSKWKFKGSDLFFGMLLFGCFVPFQVV 133 Query: 150 IYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAGFWT 209 + P+ L ++G+ T +GL++VH I+G+ TL FRNY+ +P+ L KAAR+DGAGF+T Sbjct: 134 LLPMAATLGKLGLANTTSGLVLVHVIYGVAFTTLFFRNYYVAIPDALIKAARLDGAGFFT 193 Query: 210 IYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNIVNSVQGVKEY 269 I+F+I+LPMS PIF+V++I Q T IWNDFLFGVVF + P+TV LNN+VN+ GVKEY Sbjct: 194 IFFRILLPMSTPIFMVSLIWQFTQIWNDFLFGVVFASGDSQPITVALNNLVNTSTGVKEY 253 Query: 270 NVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 NV+MAA ++ L L VY V+G+ F+RG+ AG+VKG Sbjct: 254 NVDMAAAMIAALPTLVVYIVAGKYFIRGLTAGSVKG 289 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: 314 Number of extensions: 10 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: 289 Length adjustment: 26 Effective length of query: 279 Effective length of database: 263 Effective search space: 73377 Effective search space used: 73377 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