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 AZOBR_RS06955 AZOBR_RS06955 sugar ABC transporter permease
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__azobra:AZOBR_RS06955 Length = 362 Score = 177 bits (448), Expect = 5e-49 Identities = 104/337 (30%), Positives = 176/337 (52%), Gaps = 10/337 (2%) Query: 11 PLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIALGFAV 70 PL++V L + G ++ G+DP+ A F SL+ +GE+ +PL+L A+G A+ Sbjct: 21 PLLAVALTLASGFLLFWAMGFDPVKALHAFFIAPLLSLRGLGELAVKATPLVLCAIGLAI 80 Query: 71 ASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGGVVGAIPGFLR 130 RA +NIG GQ G I G ALA ++ + ++ G A G + AIP FLR Sbjct: 81 GFRANVWNIGAEGQLTLGAITGGGLALAFYGEGGWWLLPLMIVAGMAGGALWAAIPAFLR 140 Query: 131 AYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASYQTEWLRALTN 190 SE++ ++M+NY+ L++ N ++ + R+ D + L L Sbjct: 141 VRFNASEILTSLMLNYVALHLLNYLMHGPY-----RDPDGFAFPESRLFEADAVLPLLVA 195 Query: 191 NSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTIVLSMIISG 250 +R+++G A++A+ W+L+ +T +GF+I+ +GL P A+ YAG + K+ I L++++SG Sbjct: 196 GTRVHLGSLFALLAVAAGWFLMARTFIGFQIKVIGLTPTAAGYAGFNQKKIIWLTLLLSG 255 Query: 251 ALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLFGALSVGAP 310 ALAGL G+ E G G + T S G+ + V+ L P+GI L+ FL +G Sbjct: 256 ALAGLAGLGEVAGPIGQMN-PTISPGYGYTAIIVAFLGRLHPVGILLAGFLMALSFIGGE 314 Query: 311 GMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHY 347 I+ +G P + V +++FF+ A ++ Y Sbjct: 315 AAQIA----LGLPKAITGVFQGMLLFFLLATDVLIRY 347 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: 362 Number of extensions: 24 Number of successful extensions: 3 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: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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