Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate BWI76_RS00665 BWI76_RS00665 rhamnose ABC transporter substrate-binding protein
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__Koxy:BWI76_RS00665 Length = 328 Score = 127 bits (319), Expect = 4e-34 Identities = 95/303 (31%), Positives = 151/303 (49%), Gaps = 9/303 (2%) Query: 15 LTVGVIAAAQAATNET-IVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAYQTGPGRADAA 73 LTV ++A + +A E I V K G +F + G +E AK+ V TGP A Sbjct: 9 LTVAILALSGSALAEVKIALVAKSLGNGFFEAANVGAQEAAKELGDVKVIYTGPTTTTAE 68 Query: 74 QQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNAK-NTMVDIEAF 132 Q++++ LIA+ V+AIA+ DP + P LKKAM RGIKVV+ ++ A + + Sbjct: 69 AQIEVLNGLIAQGVDAIAISANDPDAVVPVLKKAMQRGIKVVSWDSGVAPAGRQIHLNPS 128 Query: 133 DNTAYGAGLNERLASCMH----NEGKWAVLVGSLGSRSQVQWADGGIGNAKAKYAKMNLV 188 +N G + A + +G A+L + S +Q W + + +Y +NLV Sbjct: 129 NNALIGETNVKLAADALKALNVEKGDVAILSATPTSTNQNIWIEE-MKKVLPQYPSVNLV 187 Query: 189 EPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKICVYGTG 248 ++ +++Y A +L+ +PDLK SS+ ++ +AV++ G GK+ V G G Sbjct: 188 TVAYG-DDLSDKSYREAVGLLKSYPDLKVIVSPSSVGIVAAAQAVKDQGKIGKVYVTGLG 246 Query: 249 LPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADLGIPGYTKVTVAK 308 LP+E ++SGA A W+P G A +A LV G + A++G G K+ A Sbjct: 247 LPSEMAGAIKSGASKSFAIWNPIDLGYAATYLADDLVKGTATKTEANMGKLGKVKLD-AD 305 Query: 309 GPG 311 G G Sbjct: 306 GSG 308 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: 254 Number of extensions: 13 Number of successful extensions: 2 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: 334 Length of database: 328 Length adjustment: 28 Effective length of query: 306 Effective length of database: 300 Effective search space: 91800 Effective search space used: 91800 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