Align RnsA, 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 SMc02884 SMc02884 lipoprotein
Query= TCDB::Q8DU36 (349 letters) >FitnessBrowser__Smeli:SMc02884 Length = 330 Score = 144 bits (362), Expect = 4e-39 Identities = 111/341 (32%), Positives = 167/341 (48%), Gaps = 35/341 (10%) Query: 15 VLGLAACGNRAAREKGKAKTDLKVAIVTDTGGVDDKSFNQSAWEGLQAWGKDNGLSKGNG 74 +LGL A +A D+K AI+ D GG DKSFN++A+ G + + + G+ Sbjct: 5 ILGLLAFSMMSATALA---ADIKPAIIYDLGGKFDKSFNEAAFNGAEKFKTETGIE---- 57 Query: 75 FDYFQSASESDYATNLDTASSSGYKLIFGIGYALHDAIEKTAADNKNIHYVIIDDVIQKK 134 + F+ A+++ L +S G I G+ ++EK A + + + IID V++K Sbjct: 58 YREFEIANDAQREQALRRFASDGNSPIVMAGFNWAASLEKLAGEYPDTKFAIIDMVVEKP 117 Query: 135 NNVASVTFADNEAAYLAGIAAAKTTKSKKVGFVGGVKSEVITRFEKGFEAGVKSVDSSIQ 194 N V S+ F + E +YL G+ A +K+K V FVGG+ +I +F G+ G KS + ++ Sbjct: 118 N-VKSIVFKEQEGSYLVGVLAGLASKTKTVSFVGGMDIPLIHKFACGYVGGAKSTGADVK 176 Query: 195 IQVDYAG----SFGDAAKGKTIAAAQYASGADVIYQAAGGTGAGVFSEAKAVNEKKKENK 250 + Y G ++ D KG IA +Q G+DV+Y AAGGTG GV A + Sbjct: 177 VLEAYTGTTPDAWNDPVKGGEIAKSQIDQGSDVVYHAAGGTGVGVLQAAADAGKLG---- 232 Query: 251 KVWVIGVDRDQAAEGKYTSKDGKKSNFVLASSLKEVGKAVQLISTNTSKKKFPGGKVTTY 310 IGVD +Q + GK VL S LK V AV KF G ++ Sbjct: 233 ----IGVDSNQ-----NMLQPGK----VLTSMLKRVDVAVYDSFMAAKDDKFEFG-ISNL 278 Query: 311 GLKDKGVDLV-----PTHLSKEGKKAVDDAKKKIVSGDVKV 346 GLK+ GV ++ E K+AV+ K I+SG V+V Sbjct: 279 GLKEDGVGYALDEHNQVLITPEMKEAVEKVKADIISGKVQV 319 Lambda K H 0.310 0.128 0.352 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: 280 Number of extensions: 13 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: 349 Length of database: 330 Length adjustment: 28 Effective length of query: 321 Effective length of database: 302 Effective search space: 96942 Effective search space used: 96942 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 bits) S2: 49 (23.5 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