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 8502320 DvMF_3028 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Miya:8502320 Length = 308 Score = 176 bits (445), Expect = 8e-49 Identities = 115/321 (35%), Positives = 170/321 (52%), Gaps = 26/321 (8%) Query: 1 MSLENMLALLISSMLVYA-TPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEF 59 M ++ L L I + V + TP++F ++G +F+ERSGV+N+G+EG+M++GAF+G + Sbjct: 1 MDMDTALLLSILAATVQSGTPILFATLGEMFTERSGVLNLGVEGMMIVGAFSGFLVT--- 57 Query: 60 AHSFGKATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKAL 119 H G PW L GL G SLLH + + F+ + +VSG L +L LA F Sbjct: 58 -HITGN--PWAGVLAAGLCGGGLSLLHGVVCLIFQGNQVVSGLALTILGLGLADFLGTPY 114 Query: 120 YNKGQTDNISQSFGKFDFPILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGL 179 T F F P+L+ IP LG IFF+ +LV YL+ L W + +T+ GL Sbjct: 115 VGITTT-----GFQAFAVPVLADIPVLGAIFFRHDALV-YLSYLLPPLFWLFMARTRPGL 168 Query: 180 RLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFI 239 LR+ GEHP AA G++ +R+ G+ G L GIGGA + + + + G G+I Sbjct: 169 ALRAAGEHPAAASAAGLSPVRIRWCGIFTGGFLAGIGGAYLSLAYTHLWTNNMTSGRGWI 228 Query: 240 ALAAMIFGKWNPIGAMLSSLFFG----LSQSLAVIGGQLPFLSKIPTVYLQIAPYALTIL 295 A+A +IF W P A+ + FG L L +G L P+ + + PYALT+L Sbjct: 229 AVALVIFAFWRPGRAVFGAYLFGGVMALQLRLQAMGANL------PSSLMLMLPYALTVL 282 Query: 296 VL---AVFFGQAVAPKADGIN 313 VL ++ G AP A G+N Sbjct: 283 VLLASSLRGGGRAAPAALGVN 303 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: 284 Number of extensions: 18 Number of successful extensions: 5 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: 308 Length adjustment: 27 Effective length of query: 291 Effective length of database: 281 Effective search space: 81771 Effective search space used: 81771 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