Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_086510783.1 BZY95_RS15420 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc04257 (305 letters) >NCBI__GCF_002151265.1:WP_086510783.1 Length = 292 Score = 304 bits (778), Expect = 2e-87 Identities = 144/286 (50%), Positives = 204/286 (71%), Gaps = 2/286 (0%) Query: 22 RRTLSRR--NIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWV 79 RRTL R ++Y L++ AL+YLLPL VM++TS+K + EI G + + P E T PW Sbjct: 7 RRTLGARLGRAMLYAVLLLAALFYLLPLAVMLITSVKPLAEITPGTLLSLPREPTLAPWG 66 Query: 80 KAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILI 139 KAW EACTG+ C+G+ F+NS+ I VP+V+IS AI ++NGYAL WRFKG++L F +++ Sbjct: 67 KAWGEACTGMRCEGIGVYFFNSIAIVVPAVLISTAIGALNGYALTKWRFKGSELLFALML 126 Query: 140 VGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKA 199 G FIP+QV++ P+ L +G+ + GLI+VH IFG+ TL FRN++ +P EL A Sbjct: 127 FGCFIPFQVVLLPMAQTLGWLGLSSSRAGLILVHVIFGIAFTTLFFRNFYVAVPTELVSA 186 Query: 200 ARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNI 259 A++DGAGF+ I+++I+LP+S PI VV++I Q T IWNDFLFGV F+ P+TV LNN+ Sbjct: 187 AKLDGAGFFRIFWRILLPVSAPIIVVSVIWQFTQIWNDFLFGVAFSAHNTQPVTVALNNL 246 Query: 260 VNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 VN+ G +EYNV+MAA ++ L L VY ++G+ FVRG+ AG+VKG Sbjct: 247 VNTSTGAREYNVDMAAAMIAALPTLIVYVLAGKYFVRGLTAGSVKG 292 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: 256 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: 292 Length adjustment: 27 Effective length of query: 278 Effective length of database: 265 Effective search space: 73670 Effective search space used: 73670 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 Apr 09 2024. 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