Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate SM_b20316 SM_b20316 sugar ABC transporter substrate-binding protein
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__Smeli:SM_b20316 Length = 333 Score = 421 bits (1083), Expect = e-122 Identities = 203/328 (61%), Positives = 251/328 (76%), Gaps = 4/328 (1%) Query: 10 LAAAALTVGVIAAAQAATNE---TIVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAYQTG 66 +AA + +G + AAQ A + ++VTVVKVTG NWF RM+EGV + KDNP V+ Q G Sbjct: 7 IAACTVALGALCAAQLAVAQDAPSVVTVVKVTGENWFTRMEEGVVAYGKDNPAVSTSQIG 66 Query: 67 PGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNAKNTM 126 P +ADAAQQL++IEDL+AK VNAIAVVP DP LE K+AM+RGIK++THEAD+ KNT Sbjct: 67 PAKADAAQQLRLIEDLVAKNVNAIAVVPMDPSALEGVFKRAMNRGIKIITHEADSLKNTQ 126 Query: 127 VDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKAKYAKMN 186 VDIEAFDN +GA NE+LA CM GKW VGSLGS + VQWADGG NAK KY +M Sbjct: 127 VDIEAFDNKVFGARFNEKLAECMGKSGKWTSFVGSLGSLTHVQWADGGAENAK-KYPEME 185 Query: 187 LVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKICVYG 246 LV K E+ ND +AYE A+E+LRK+PD+KGFQG S++DVIGIGRAVEEAG+ GK+CV G Sbjct: 186 LVSEKNESFNDANKAYEKAREILRKYPDIKGFQGGSAIDVIGIGRAVEEAGLVGKVCVVG 245 Query: 247 TGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADLGIPGYTKVTV 306 GLP + K+LESGA+ I+FWDPK AG MNKVA+++++GK + +G DLG+PGY KV+V Sbjct: 246 LGLPKDTAKYLESGAVQSISFWDPKDAGYVMNKVAQLVIEGKEITDGMDLGVPGYNKVSV 305 Query: 307 AKGPGKGIIVRGQGWVNVDKSNYKQYPF 334 GPG GIIV G+ WV+VDKSNY QYPF Sbjct: 306 KNGPGDGIIVVGEAWVDVDKSNYSQYPF 333 Lambda K H 0.314 0.133 0.385 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: 412 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 334 Length of database: 333 Length adjustment: 28 Effective length of query: 306 Effective length of database: 305 Effective search space: 93330 Effective search space used: 93330 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: 42 (22.0 bits) S2: 49 (23.5 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