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_RS06630 AZOBR_RS06630 sugar ABC transporter permease
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__azobra:AZOBR_RS06630 Length = 363 Score = 182 bits (463), Expect = 9e-51 Identities = 119/348 (34%), Positives = 181/348 (52%), Gaps = 13/348 (3%) Query: 9 VVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIALGF 68 ++PL++++ ++L +++++ G +P+ L +A G + IG + I L Sbjct: 9 LLPLLNLLAALVLSGLVILVIGENPLDVLALLVTEAVGYPEAIGYTLYYTTSYIFTGLAV 68 Query: 69 AVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGGVVGAIPGF 128 A+A G FNIG GQAY G + AG LA P P+ L V + A G V AIPG+ Sbjct: 69 AIAFHCGLFNIGGEGQAYLGGLGAGLVGLALTGWPWPVAALGAVALSALFGAVWAAIPGW 128 Query: 129 LRAYLGTSEVIVTIMMNYIVLYI-----GNAIIQDGFAKNIMRNSDSSIYVGHNASYQTE 183 L+A G+ VI TIM N+I I + +I+ G R D +++ Sbjct: 129 LQAKRGSHIVITTIMFNFIAAAIMTYLLVDVLIRPGSQSPETREFDPGVWL-PTMDRAVG 187 Query: 184 WLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTIV 243 W+ S +N+ F A+ + + L +T G+EIR+VG N A+ YAG+S R I+ Sbjct: 188 WIGVAIPVSPLNLSFLWALACCALFYLFLWRTRWGYEIRTVGRNERAAVYAGISPARNII 247 Query: 244 LSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLFG 303 L+M ISGALAG GV E +G + + + +GF G+AV+L+ N P+GI L+A LFG Sbjct: 248 LAMAISGALAGFVGVNEIMGVQHRILLNFTG-GVGFVGIAVALMGRNHPVGIILAALLFG 306 Query: 304 ALSVGAPGMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHYIKPR 351 L+ G +S T EL+ V+ L+I F GA +E+ KPR Sbjct: 307 VLAQGGGQVSFEYPT---VNRELVMVIQGLVILFAGA---LENLFKPR 348 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: 359 Number of extensions: 28 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: 363 Length adjustment: 29 Effective length of query: 329 Effective length of database: 334 Effective search space: 109886 Effective search space used: 109886 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