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 SMc04125 SMc04125 ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Smeli:SMc04125 Length = 323 Score = 212 bits (540), Expect = 8e-60 Identities = 120/329 (36%), Positives = 189/329 (57%), Gaps = 17/329 (5%) Query: 1 MSLENMLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFA 60 M ++L +L+ S + + PL+F ++ G+F+ER+GV ++GLEG M+ AFA A Sbjct: 1 MDFFHVLVVLLESTIRVSVPLVFAALAGLFTERAGVFDIGLEGKMLGAAFAAG------A 54 Query: 61 HSFGKATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALY 120 + + W+ LV + SL+H A+I R + IVSG +N + V +A + Sbjct: 55 AAAVTQSVWVGLGAAILVSVALSLVHGYASITQRGNQIVSGVAINFIVAGSTVILGEAWF 114 Query: 121 NKG-QTDNISQS--FGKFDFP---ILSHIPFLGPIF---FQGTSLVAYLAVLFSVFAWFI 171 +G +T +++ F +FP ++ IP LGP++ G L+ YLA +W+I Sbjct: 115 RQGGRTPALAEGARFQTINFPDADMIREIPVLGPVYADLLSGHFLLTYLAFAMVPISWWI 174 Query: 172 LTKTKFGLRLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGT 231 L +T+FGLRLR+VGE+P A DT GI+V +RY V+ G+L G GA + +++ F Sbjct: 175 LYRTRFGLRLRAVGENPGAVDTAGISVIWLRYRAVICCGILCGFAGAYLSLAMTAGFVKG 234 Query: 232 TILGPGFIALAAMIFGKWNPIGAMLSSLFFGLSQSLAV--IGGQLPFLSKIPTVYLQIAP 289 G G+IALAA+IF KW P+ M + L FG +LA+ G LP + ++P +Q P Sbjct: 235 MTAGKGYIALAALIFAKWRPLNIMFACLLFGFLDALAIRLQGTPLPLVGQVPVQLMQALP 294 Query: 290 YALTILVLAVFFGQAVAPKADGINYIKSK 318 Y LT+++LA F G+A+ PKA G+ Y+K + Sbjct: 295 YILTVILLAGFIGKAIPPKAGGVPYVKER 323 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: 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: 323 Length adjustment: 28 Effective length of query: 290 Effective length of database: 295 Effective search space: 85550 Effective search space used: 85550 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