Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_03822 H281DRAFT_03822 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:D8IUD0 (314 letters) >FitnessBrowser__Burk376:H281DRAFT_03822 Length = 320 Score = 300 bits (768), Expect = 3e-86 Identities = 163/316 (51%), Positives = 214/316 (67%), Gaps = 3/316 (0%) Query: 1 MNKFTRRHFAIA-ALACAVLPGAAMAQTP--AKPKVALVMKSLANEFFLNMENGAREYQK 57 M + RR IA ALA A L AA A T PK+ALV+KS+ + F + M N A+ YQ+ Sbjct: 1 MTQEMRRRVLIAGALAAAGLTRAAGAATVEGGMPKIALVLKSINDPFTVAMANAAKNYQQ 60 Query: 58 ANASKFDLIANGIKDEQDTANQIKIVEQMIVSKVNALVIAPADSKALVPVVKKAIDAGII 117 AS+F L G E DTA QI+IV+ +I +K+NA+VIAP+ SK L VV +AI AGII Sbjct: 61 HYASQFALTVRGTATEADTAGQIRIVDDLIKAKMNAIVIAPSGSKPLTAVVARAIKAGII 120 Query: 118 VVNIDNKLDDAALKEKGITVPFVGPDNRKGAKLAGDYLGKQLQKGDKVAIIEGVSTTFNA 177 VV+IDN LDDA+ I+VPFVGPDNRKGA L +YL +LQ GD+V IIEG++ NA Sbjct: 121 VVSIDNPLDDASQDAAKISVPFVGPDNRKGATLVANYLAGRLQAGDQVGIIEGIAADRNA 180 Query: 178 QQRTLGFQDAMKDVGANVVTVQSGQWEIDQGNKVAASILNAHPDIKAILAGNDNMALGAV 237 Q+RT G++D M G VV Q+ WE +G VA+ +L HP I+ +L NDNMA+GA Sbjct: 181 QERTAGYRDVMSTAGMQVVATQAADWEYGKGRDVASKMLGQHPQIRGLLCANDNMAMGAA 240 Query: 238 AAIRAAGKTGKVQLVGYDNINAIKPMLKDGRVLATVDQFAQQQAVFGIETALKALSEKKP 297 A+R AG+TG V + GY+ I AIKP++ DG VLATV+QFA +QAVFG++ ALKA++E++ Sbjct: 241 DAVRDAGRTGGVYITGYNAIEAIKPLIADGHVLATVNQFADRQAVFGMDVALKAVTEQRK 300 Query: 298 QSALGGVVETKVSLVT 313 Q L +ET + LVT Sbjct: 301 QRELSRTIETPLQLVT 316 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: 237 Number of extensions: 5 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: 320 Length adjustment: 27 Effective length of query: 287 Effective length of database: 293 Effective search space: 84091 Effective search space used: 84091 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