Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate BPHYT_RS25795 BPHYT_RS25795 LacI family transcription regulator
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__BFirm:BPHYT_RS25795 Length = 334 Score = 648 bits (1672), Expect = 0.0 Identities = 323/334 (96%), Positives = 329/334 (98%) Query: 1 MKLTRLGAALAAAALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDEGVKEFAKDNPGV 60 MKLTRLGAALAA ALTVGVIAAAQAATNETIVTVVKVTGINWFNRMD+GVK+FAKDNP + Sbjct: 1 MKLTRLGAALAAGALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDDGVKQFAKDNPNI 60 Query: 61 TAYQTGPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEAD 120 AYQTGPGRADAAQQLKIIEDLIAKKV AIAVVPYDPPTLEPALKKAMDRGIKVVTHEAD Sbjct: 61 NAYQTGPGRADAAQQLKIIEDLIAKKVTAIAVVPYDPPTLEPALKKAMDRGIKVVTHEAD 120 Query: 121 NAKNTMVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKA 180 NAKNTMVDIEAFDNTAYGAGLNERLASCMH++GKWAVLVGSLGSRSQVQWADGGIGNAKA Sbjct: 121 NAKNTMVDIEAFDNTAYGAGLNERLASCMHDDGKWAVLVGSLGSRSQVQWADGGIGNAKA 180 Query: 181 KYAKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQG 240 KY KMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQG Sbjct: 181 KYPKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQG 240 Query: 241 KICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDGKTVENGADLGIPG 300 KICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVA+MLVDGKTVENGADLGIPG Sbjct: 241 KICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAQMLVDGKTVENGADLGIPG 300 Query: 301 YTKVTVAKGPGKGIIVRGQGWVNVDKSNYKQYPF 334 YTKVTVAKGPGKGIIVRGQGWVNVDKSNYKQYPF Sbjct: 301 YTKVTVAKGPGKGIIVRGQGWVNVDKSNYKQYPF 334 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: 534 Number of extensions: 10 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: 334 Length of database: 334 Length adjustment: 28 Effective length of query: 306 Effective length of database: 306 Effective search space: 93636 Effective search space used: 93636 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