Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_094506794.1 CEV31_RS09340 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc04257 (305 letters) >NCBI__GCF_002252445.1:WP_094506794.1 Length = 293 Score = 288 bits (736), Expect = 1e-82 Identities = 136/276 (49%), Positives = 192/276 (69%) Query: 30 IIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWVKAWAEACTGL 89 +++Y L++ A YYLLPLYVM+V S K + EIR G + + P + T EPW+ AW+ A G+ Sbjct: 18 VLIYSALLLFAFYYLLPLYVMLVNSFKPLDEIRQGGMLSLPQQWTIEPWLSAWSTAQIGV 77 Query: 90 NCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQVM 149 GL F NS+ + VP+V IS + ++NGY L WRF+G+++FF +L++ F+P+Q++ Sbjct: 78 QPTGLKPFFINSILMVVPAVAISTIVGALNGYVLTKWRFRGSNIFFGLLLLSCFMPFQIV 137 Query: 150 IYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAGFWT 209 + P+ VL +G+ GT+ GLI+VH ++G+ TL FRNY+ P EL +AA++DGA F+ Sbjct: 138 LIPMARVLGMLGIAGTIWGLILVHVVYGIGFTTLYFRNYYEAFPTELVRAAQIDGASFFQ 197 Query: 210 IYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNIVNSVQGVKEY 269 I+++I+LP S PI VV++I Q T IWNDFLFG F+ PMTV LNN+V+S GVKEY Sbjct: 198 IFWRILLPSSGPIIVVSVIWQFTNIWNDFLFGASFSGAHSTPMTVALNNLVSSSTGVKEY 257 Query: 270 NVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 NV+ A IL L L VY VSGR FVRG+ +GAVKG Sbjct: 258 NVHFAGAILAALPTLIVYIVSGRYFVRGLMSGAVKG 293 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: 281 Number of extensions: 11 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: 293 Length adjustment: 27 Effective length of query: 278 Effective length of database: 266 Effective search space: 73948 Effective search space used: 73948 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 24 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