Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS20560 BPHYT_RS20560 sugar ABC transporter substrate-binding protein
Query= uniprot:D8IUD0 (314 letters) >FitnessBrowser__BFirm:BPHYT_RS20560 Length = 316 Score = 317 bits (813), Expect = 2e-91 Identities = 169/311 (54%), Positives = 226/311 (72%), Gaps = 3/311 (0%) Query: 6 RRHFAIA-ALACAVLPGAA-MAQTPA-KPKVALVMKSLANEFFLNMENGAREYQKANASK 62 RR IA ALA A + GAA A TP K K+ALV+KSL + F + M + A+ YQ+ AS+ Sbjct: 2 RRRVVIAGALAAAGIGGAADAAATPGGKLKIALVLKSLGDPFTIAMASAAQNYQQHYASQ 61 Query: 63 FDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGIIVVNID 122 FDL G E DT QI++VE+MI +K+NA+VIAP DSKAL VV +AI AG+IVV+ID Sbjct: 62 FDLTVRGTATESDTTGQIRMVEEMIKAKMNAIVIAPTDSKALTAVVARAIKAGVIVVSID 121 Query: 123 NKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNAQQRTL 182 N LD+A GI+VPFVGP+NRKGA+ +YL ++L+ GD+V +IEG S NAQQRT Sbjct: 122 NPLDEAFQDAAGISVPFVGPNNRKGAQQVSNYLAERLKTGDQVGVIEGSSADRNAQQRTD 181 Query: 183 GFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAVAAIRA 242 G +DAM G N+V VQ+G WE +G A+ +L+ HP I+ ++ GNDNMA+GAV A+R Sbjct: 182 GCRDAMNAAGINIVAVQTGDWEYGKGRDAASKMLSEHPQIRGLMCGNDNMAMGAVDAVRD 241 Query: 243 AGKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKPQSALG 302 AG+TG V + GY++I+AIKP++ DGRVLATV+QFA +QAVFG++ ALKA++E++ QS L Sbjct: 242 AGRTGGVYVTGYNDIDAIKPLIADGRVLATVNQFAARQAVFGVDVALKAVTEQRKQSELS 301 Query: 303 GVVETKVSLVT 313 V+ET + LVT Sbjct: 302 SVIETPLQLVT 312 Lambda K H 0.315 0.131 0.355 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: 255 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: 314 Length of database: 316 Length adjustment: 27 Effective length of query: 287 Effective length of database: 289 Effective search space: 82943 Effective search space used: 82943 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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