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 SM_b20125 SM_b20125 sugar ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Smeli:SM_b20125 Length = 310 Score = 194 bits (493), Expect = 2e-54 Identities = 123/314 (39%), Positives = 170/314 (54%), Gaps = 12/314 (3%) Query: 5 NMLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFG 64 + LA I++ A PL+F SIG VFSER+GV+N+GLEG+M+ GAFAG FA +F Sbjct: 8 SFLAATIAASWRLAAPLMFASIGEVFSERAGVLNIGLEGVMLAGAFAG------FAAAFT 61 Query: 65 KATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNK-G 123 + + G+L LL A TI +AD IV G +NLL L F +A ++ G Sbjct: 62 SGSILLGVAAAVAAGVLVGLLFAFFTITIKADQIVVGAAINLLGLGLTAFLFRAYFSSAG 121 Query: 124 QTDNISQSFGKFDFPILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRS 183 + I++ D P LS +PF G FF+ + V Y + + A F+L +T FGL LR+ Sbjct: 122 KGIEIAKPV---DLPWLSDLPFFGEAFFRQNAFV-YSTLPVAALAVFVLYRTSFGLTLRA 177 Query: 184 VGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAA 243 VGEHP+A D G +V L RY V+I L +GGA + S F G GFIALA Sbjct: 178 VGEHPKAVDVSGRSVALYRYGAVLICSALAALGGAFLTLAHSNQFVEGISSGRGFIALAV 237 Query: 244 MIFGKWNPIGAMLSSLFFGLSQSLAVIGGQLPFLSKIPTVYLQIAPYALTILVLAVFFGQ 303 ++F +W+PIGA + SL FG+ +L + P L +P Q PY +TI L + + Sbjct: 238 VVFARWSPIGAFIVSLLFGVFYALQLQLQAQPVLF-LPYQLFQALPYVMTIAALILVRNR 296 Query: 304 AVAPKADGINYIKS 317 P G+ Y KS Sbjct: 297 VDTPSMLGVAYKKS 310 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: 267 Number of extensions: 12 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: 310 Length adjustment: 27 Effective length of query: 291 Effective length of database: 283 Effective search space: 82353 Effective search space used: 82353 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