Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate RR42_RS04820 RR42_RS04820 choline ABC transporter permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__Cup4G11:RR42_RS04820 Length = 215 Score = 105 bits (261), Expect = 1e-27 Identities = 66/194 (34%), Positives = 106/194 (54%), Gaps = 5/194 (2%) Query: 149 LALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDAMQTTPA---FVYLVPIVMLFG- 204 LALV +++ IV+G+PLGI AR A + L + T P+ F ++PI FG Sbjct: 22 LALVGSSVGLAIVVGVPLGILCARFRFLATPLLTLATIVLTLPSIALFGLMIPIFARFGH 81 Query: 205 -IGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLFKVQLPLAMPT 263 +G VP V +++L PI+R T + + V + EA R G + Q + V LPLA+P Sbjct: 82 ALGYVPAVTAVFLYSLLPIMRNTCVALANVDDGIQEAGRGIGMTTWQRMRLVDLPLAVPV 141 Query: 264 IMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLATVGGVGIVILAIILDRL 323 I+ GV +++ + + IA++I GGLG ++L+ I + +M +G V + +LAI+ D Sbjct: 142 ILGGVRTAVVMNIGVATIAAIIGAGGLGVLILQAISQSNMSKLAIGAVLVSVLAIVADAC 201 Query: 324 TQAVGRDSRSRGNR 337 Q + R +G R Sbjct: 202 LQWLQRVLTPKGIR 215 Lambda K H 0.326 0.141 0.435 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: 224 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 354 Length of database: 215 Length adjustment: 25 Effective length of query: 329 Effective length of database: 190 Effective search space: 62510 Effective search space used: 62510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 47 (22.7 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