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 AZOBR_RS31890 AZOBR_RS31890 ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__azobra:AZOBR_RS31890 Length = 305 Score = 134 bits (336), Expect = 4e-36 Identities = 100/326 (30%), Positives = 157/326 (48%), Gaps = 35/326 (10%) Query: 4 ENMLALLISS-----MLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIE 58 + +L +L+S+ +L ATP I ++G + ER+GV+N+G+EGIM MGA AG Sbjct: 3 QTILDILVSAAFWTAVLRIATPYILGTLGELLCERAGVLNLGIEGIMTMGAMAG------ 56 Query: 59 FAHSFGKATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKA 118 + + A W LV L G L LLHA T+ V+G + LL SL+ F + Sbjct: 57 WMAVYQGADLWTGVLVAALCGGLMGLLHATLTVPLGLSQHVAGIGVTLLGTSLSYFVYRL 116 Query: 119 LYNKGQTDNISQSFGKFDFP-ILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKF 177 + + T + F D P L+ P + Y+A++ ++L +T Sbjct: 117 VLPQASTPPTIEPFQPLDLPGALAQTP------------MTYMALMLVAVVAYVLYRTPV 164 Query: 178 GLRLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPG 237 GL +R VGE+P AA+ G++V +R V+ L + GA S F + G G Sbjct: 165 GLAVRMVGENPAAAEAQGLSVTAVRIGAVVAGSALMALAGAFLTLSAFNAFFFNMVNGRG 224 Query: 238 FIALAAMIFGKWNPIGAMLSSLFFGLSQSL-----AVIGGQLPFLSKIPTVYLQIAPYAL 292 +I +A ++F W P A+L ++ F +L V GG LP+ ++L + PY L Sbjct: 225 WICIALVVFASWRPGKALLGAVLFAAFDALQLRLQQVAGGVLPY-----QLFLMM-PYLL 278 Query: 293 TILVLAVFFGQAVAPKADGINYIKSK 318 +IL L + +A P+A I Y K + Sbjct: 279 SILALVLVARRASYPRALMIPYRKGE 304 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: 230 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: 305 Length adjustment: 27 Effective length of query: 291 Effective length of database: 278 Effective search space: 80898 Effective search space used: 80898 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