Align deoxynucleoside transporter, substrate-binding component (characterized)
to candidate 3609045 Dshi_2434 rhamnose ABC transporter, periplasmic rhamnose-binding protein (RefSeq)
Query= reanno::Burk376:H281DRAFT_01114 (334 letters) >FitnessBrowser__Dino:3609045 Length = 333 Score = 129 bits (323), Expect = 1e-34 Identities = 95/305 (31%), Positives = 150/305 (49%), Gaps = 6/305 (1%) Query: 4 TRLGAALAAAALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDEGVKEFAKDNPGVTAY 63 T+L A L+ AA G A AQ I VVK GI +F +G +E A + GV Sbjct: 7 TKLTAGLSLAASLFGTTAMAQDEMR--IALVVKALGIGFFEAAAQGAEEAAAELGGVEII 64 Query: 64 QTGPGRADAAQQLKIIEDLIAKKVNAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNA- 122 TGP A Q+++I LIA+ V+AIAV D L P LKKAM RGI V++ ++ A Sbjct: 65 YTGPTDTTAEGQIEVINSLIAQGVDAIAVSANDTDALVPTLKKAMQRGITVISWDSGVAP 124 Query: 123 KNTMVDIEAFDNTAYGAGLNERLASCMHNEGKWAVLVGSLGSRSQVQWADGGIGNAKAKY 182 + + + N G + + A + + G AVL + S +Q W + + Y Sbjct: 125 EGRQMHLNPSSNALIGNMIIKLAADHLPDGGDVAVLSATTTSTNQNIWIE-EMTKVLGDY 183 Query: 183 AKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQGKI 242 +N+V + ++ +++Y A+ +++ PDL +S+ ++ +AV +AG G++ Sbjct: 184 PGINVVS-TVYGDDLADKSYREAQGLMQSFPDLDAIIAPTSVGIVAAAQAVADAGKIGQV 242 Query: 243 CVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAKMLVDG-KTVENGADLGIPGY 301 V G GLP+E +ESGA A W+P G + +A L G T E G ++ I Sbjct: 243 NVTGLGLPSEMAGAIESGASKSFAIWNPIDLGYSAAMIAHALASGAATAEPGTEISIGRV 302 Query: 302 TKVTV 306 +T+ Sbjct: 303 GTITL 307 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: 228 Number of extensions: 15 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: 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