Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate H281DRAFT_01452 H281DRAFT_01452 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_01452 Length = 305 Score = 370 bits (951), Expect = e-107 Identities = 174/287 (60%), Positives = 223/287 (77%) Query: 19 RKPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPW 78 R+ R + + VY L+ AL++LLPLYVM+VTS K M EIR+GN+ A P T W Sbjct: 19 RRRRTAFTPARVGVYLFLLSAALFFLLPLYVMLVTSFKPMSEIRLGNLLALPAHFTLHAW 78 Query: 79 VKAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTIL 138 AW ACTGL+C+G+ GFWNSVRI VPS + SIAI +VNGYAL+ WR +GA + F +L Sbjct: 79 SAAWESACTGLDCNGIQVGFWNSVRIVVPSTVFSIAIGAVNGYALSFWRPRGAGVLFGVL 138 Query: 139 IVGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFK 198 ++GAFIP QVM+YP+V VL + ++ +L G++++HTIFGMP++TLLFRNY+A +P+ELFK Sbjct: 139 LMGAFIPVQVMVYPLVRVLASVHLFSSLPGIVVIHTIFGMPVMTLLFRNYYASIPQELFK 198 Query: 199 AARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNN 258 AAR+DG GFW I+ ++MLPMS PI VVA+I+QVTGIWNDF+ G+VF + PMTVQLNN Sbjct: 199 AARIDGGGFWRIFVQLMLPMSTPIIVVAVIMQVTGIWNDFILGLVFAGTKNLPMTVQLNN 258 Query: 259 IVNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 I+N+ G + YNVNMAATILT LVPL VYF+SGR FVRGIA+GAVKG Sbjct: 259 IINTTTGERLYNVNMAATILTSLVPLAVYFISGRWFVRGIASGAVKG 305 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: 345 Number of extensions: 8 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: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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