Align RnsC, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate 3608552 Dshi_1946 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__Dino:3608552 Length = 349 Score = 146 bits (369), Expect = 7e-40 Identities = 98/311 (31%), Positives = 160/311 (51%), Gaps = 10/311 (3%) Query: 5 TQKLVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILI 64 T+ L +P +++ L +I + + ++ G DP + Q A GS + E +PLI Sbjct: 12 TRTLGLPAVALTLTVIAASGLALVAGGDPFAVLGLIVQGAVGSKFALLETLNRATPLIFT 71 Query: 65 ALGFAVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAA--SGGVV 122 L AVA RA +NIG Q Y G + L LP P +L+ VL+ A+ +G ++ Sbjct: 72 GLAVAVAFRAKLWNIGAEAQLYGGAVIT--VVLGTGFLPWPAGVLLPVLVIASMLTGALL 129 Query: 123 GAIPGFLRAYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASYQT 182 P +L+ LG EV+ T+++N+I L + +++ + S + A Sbjct: 130 LLGPAYLKTRLGVDEVVTTLLLNFIALLFVSMLLEGPLKDPMGMGWPKSERLIPEAR--- 186 Query: 183 EWLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTI 242 L L + R++ GF LA+IA VW + +TTLG+E+R+VG NP A+ +AG+ I Sbjct: 187 --LPRLVDGLRLHWGFALALIAAAAVWVIQTRTTLGYEMRAVGQNPDAARFAGIPVGAVI 244 Query: 243 VLSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLF 302 + + +SG LA L G E G G++ + S G+ G+ V++LA +P+G+ +SA Sbjct: 245 LKTAFLSGGLAALAGFSEVAGLKGSLTLDLSP-GFGYTGIIVAMLALLNPLGVVVSALFV 303 Query: 303 GALSVGAPGMS 313 + VGA MS Sbjct: 304 AGVFVGADSMS 314 Lambda K H 0.325 0.141 0.416 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: 299 Number of extensions: 16 Number of successful extensions: 4 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: 358 Length of database: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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