Align RnsD, 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 HSERO_RS07090 HSERO_RS07090 ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__HerbieS:HSERO_RS07090 Length = 306 Score = 126 bits (316), Expect = 8e-34 Identities = 94/294 (31%), Positives = 135/294 (45%), Gaps = 19/294 (6%) Query: 6 MLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGK 65 +L L + + TP +F S+G +E+ G VN+GLEGI+V GA G +A SF Sbjct: 9 LLLALFAGAIRVGTPFLFVSLGECLTEKGGRVNLGLEGILVCGAMTG------YAASFYS 62 Query: 66 ATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKGQT 125 + W+ L G GLL +LH + R + I G L LL LA F K Sbjct: 63 GSAWLGVLAAGCTGLLLGVLHGVVCSLPRVNDIAFGIALMLLGTGLAFFLGKPFIQPQAP 122 Query: 126 DNISQSFGKFDF-PILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRSV 184 S G + L H + +FF G VL V W L+ T++GL LR V Sbjct: 123 MLPSIDLGAWSSNDRLHHALQINALFFIG-------VVLALVLQWG-LSATRWGLALRLV 174 Query: 185 GEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAAM 244 G+H + A LG + R G L +GGA + ++ G G +A+A + Sbjct: 175 GDHAETARALGYRLTGTRIAATAAGGFLAAVGGAYLSLYYPGSWNEGLSSGQGLMAVALV 234 Query: 245 IFGKWNPIGAMLSSLFFGLSQSLAVIGGQLPFLSKIPTVYL-QIAPYALTILVL 297 IF +W P +L++L FG + +L G L + YL APYALT+L++ Sbjct: 235 IFARWQPWRCLLAALLFGAAGAL---GPALQAVGVTSGYYLFNAAPYALTLLIM 285 Lambda K H 0.328 0.143 0.422 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: 243 Number of extensions: 14 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: 318 Length of database: 306 Length adjustment: 27 Effective length of query: 291 Effective length of database: 279 Effective search space: 81189 Effective search space used: 81189 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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