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 GFF2773 PGA1_c28160 ABC transporter, permease protein
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Phaeo:GFF2773 Length = 306 Score = 155 bits (392), Expect = 1e-42 Identities = 100/312 (32%), Positives = 157/312 (50%), Gaps = 17/312 (5%) Query: 9 LLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGKATP 68 LLI+S++V ATP++ +IG + E+SGV+N+G+EG+M+ GA AG FA + +P Sbjct: 10 LLIASLMVAATPILIAAIGELVVEKSGVLNLGVEGMMITGAIAG------FATAVETGSP 63 Query: 69 WIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKGQTDNI 128 + G S+L T +A+ + SG L L L+ AL + Sbjct: 64 LLGFFAAAFAGAALSVLFGFLTQFAKANQVASGLALTLFGLGLS-----ALMGQSYVGVK 118 Query: 129 SQSFGKFDFPILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRSVGEHP 188 G P+LS +P +GPI F G ++ Y + + W +L ++ GL LR+VGE+ Sbjct: 119 PPQMGDIHIPVLSDLPVVGPILF-GHDIILYFGIALTAAVWALLKFSRAGLILRAVGENH 177 Query: 189 QAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAAMIFGK 248 AA LG V +R + ++ G G+GGA + + G G+IALA ++F Sbjct: 178 DAAHALGYKVIRIRLMAILFGGACAGVGGAYISLIRVPQWTEGMTAGVGWIALALVVFAS 237 Query: 249 WNPIGAMLSSLFFGLSQSLAVIGGQLPFLS-KIPTVYLQIAPYALTILVLAVFFG-QAVA 306 W P A+L + FG + V+ L IP YL ++PY +TI+VL + ++ A Sbjct: 238 WKPWRALLGAYLFG---GVTVVQLNLQAAGVAIPVEYLAMSPYVITIVVLVILSADKSSA 294 Query: 307 PKADGINYIKSK 318 P A G N+ S+ Sbjct: 295 PAALGRNFHASR 306 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: 213 Number of extensions: 14 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: 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