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 3608551 Dshi_1945 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Dino:3608551 Length = 314 Score = 160 bits (406), Expect = 3e-44 Identities = 104/299 (34%), Positives = 151/299 (50%), Gaps = 7/299 (2%) Query: 18 ATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGKATPWIAALVGGL 77 A+PLIF ++G + ER+GV+N+G+EGIMV GAFAG + + W V Sbjct: 20 ASPLIFATMGELICERAGVLNLGIEGIMVAGAFAG------WMAVYTGTDLWTGVAVAFG 73 Query: 78 VGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKGQTDNISQSFGKFDF 137 G+LF LLHA T+ F V G + LLA S F + + + ++F ++ Sbjct: 74 AGMLFGLLHATLTVPFGLSQHVVGLGITLLATSATYFAYRVALPEVSSPPRIEAFQPYEI 133 Query: 138 PILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRSVGEHPQAADTLGIN 197 P+LS +P LGP F T L YLA + F L +T GL LR+ GE+P A + G++ Sbjct: 134 PLLSDLPLLGPALFSQTPLT-YLAFAVAGLTAFTLYRTPLGLALRAAGENPSAVEAQGLS 192 Query: 198 VYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAAMIFGKWNPIGAMLS 257 V +R V++ L +GGA S +F + G G+I +A ++FG W P A+L Sbjct: 193 VTGLRMGAVIVGSGLMAVGGAFLTMSAFNSFFFEMVNGRGWICIALVVFGAWRPGKALLG 252 Query: 258 SLFFGLSQSLAVIGGQLPFLSKIPTVYLQIAPYALTILVLAVFFGQAVAPKADGINYIK 316 +L F +L V Q + IP + PY L+IL L V +A P A + Y K Sbjct: 253 ALLFAAFDALQVRLQQTGLGADIPYQVFLMLPYILSILALIVMSRRAEVPAALMVPYNK 311 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: 255 Number of extensions: 13 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: 318 Length of database: 314 Length adjustment: 27 Effective length of query: 291 Effective length of database: 287 Effective search space: 83517 Effective search space used: 83517 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