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 3609458 Dshi_2842 basic membrane lipoprotein (RefSeq)
Query= TCDB::Q8DU36 (349 letters) >FitnessBrowser__Dino:3609458 Length = 329 Score = 129 bits (325), Expect = 8e-35 Identities = 96/317 (30%), Positives = 157/317 (49%), Gaps = 34/317 (10%) Query: 39 AIVTDTGGVDDKSFNQSAWEGLQAWGKDNGLSKGNGFDYFQSASESDYATNLDTASSSGY 98 A++ D GG DKSFN++A+ G Q W ++ G + + SE+ L + +G Sbjct: 26 ALIFDLGGKFDKSFNEAAFNGAQRWVQETG----GTYREIELTSEAQREQALRRFAEAGN 81 Query: 99 KLIFGIGYALHDAIEKTAADNKNIHYVIIDDVIQKKNNVASVTFADNEAAYLAGIAAAKT 158 I G+A + + + A D + + IID V+ + N V SV F ++E +YL G+ AA Sbjct: 82 NPIVMTGFAFGNVLGEVAPDYPDTSFAIIDMVVDQPN-VRSVVFNEHEGSYLVGMMAAMA 140 Query: 159 TKSKKVGFVGGVKSEVITRFEKGFEAGVKSVDSSIQIQVDYAG----SFGDAAKGKTIAA 214 +++ VGF+GG+ +I +F G+ GVK+ + + + G ++ D KG + Sbjct: 141 SETGTVGFIGGMDIPLIRKFACGYAQGVKAANPDATVIQNMTGTTPAAWNDPVKGGELTR 200 Query: 215 AQYASGADVIYQAAGGTGAGVFSEAKAVNEKKKENKKVWVIGVDRDQAAEGKYTSKDGKK 274 AQ + GADV+Y AAGGTG GV A ++ + IGVD +Q + Sbjct: 201 AQISQGADVVYAAAGGTGVGVLQTA--------ADEDILSIGVDSNQ---------NYLH 243 Query: 275 SNFVLASSLKEVGKAVQLISTNTSKKKFPGGKVTTYGLKDKGV-----DLVPTHLSKEGK 329 VL S +K V AV + + F G + GL + GV + ++ E + Sbjct: 244 PGEVLTSMMKRVDNAV--FAAMSDGPGFETG-IRVLGLAEDGVGYALDEFNAELVTDEMQ 300 Query: 330 KAVDDAKKKIVSGDVKV 346 AV++AK KI++G++ V Sbjct: 301 AAVEEAKAKIIAGEITV 317 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: 257 Number of extensions: 16 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: 329 Length adjustment: 28 Effective length of query: 321 Effective length of database: 301 Effective search space: 96621 Effective search space used: 96621 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