Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate SM_b20484 SM_b20484 sugar ABC transporter substrate-binding protein
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__Smeli:SM_b20484 Length = 330 Score = 190 bits (482), Expect = 5e-53 Identities = 115/291 (39%), Positives = 159/291 (54%), Gaps = 2/291 (0%) Query: 6 LGAALAAAALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAYQT 65 L AALAA+ G AA T + V VVK+ GI WFN M+ G+KE + GV A+ Sbjct: 6 LAAALAASLSLAGAYTAAAQDTGKVGV-VVKIGGIPWFNAMEAGIKERG-EKLGVDAFMV 63 Query: 66 GPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNAKNT 125 GP AD A Q++ IEDLIA+ V I VVP D LEP L KA ++GI V+THE+ + K Sbjct: 64 GPTSADPALQVRAIEDLIAQNVKVIGVVPNDAKVLEPVLTKAREKGIIVITHESPSQKGA 123 Query: 126 MVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKAKYAKM 185 D E T +G + LA M +G++AV VGSL WAD I K + +M Sbjct: 124 DWDFELASATGFGEAHAKLLAEKMGGKGEYAVFVGSLTVPLHNAWADAAIEYIKKNHPEM 183 Query: 186 NLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKICVY 245 LV + D +++ A +++ HPDLKGF S IG GRA+EE G+I V Sbjct: 184 TLVGDRYGVAEDVDKSRSTALDLISAHPDLKGFLAFGSQGPIGAGRAIEERRKVGEIFVL 243 Query: 246 GTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADL 296 G P + K ++S AI+G W+PK AG +A L+ G+ +++G ++ Sbjct: 244 GPFSPGQGQKLIKSDAISGGFMWNPKQAGEVFVTLAAKLMKGEEIKDGEEI 294 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: 287 Number of extensions: 15 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: 330 Length adjustment: 28 Effective length of query: 306 Effective length of database: 302 Effective search space: 92412 Effective search space used: 92412 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