Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate RR42_RS13780 RR42_RS13780 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >FitnessBrowser__Cup4G11:RR42_RS13780 Length = 297 Score = 494 bits (1273), Expect = e-145 Identities = 241/291 (82%), Positives = 264/291 (90%) Query: 3 TTTKPVNQKAWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVFVGTEWFAAVMRD 62 +T KPVNQKAW L++PV++CVAFSAILPLMT+VNYSVQDIISPERRVFVGTEWF V+RD Sbjct: 2 STLKPVNQKAWLLVIPVVLCVAFSAILPLMTIVNYSVQDIISPERRVFVGTEWFRTVLRD 61 Query: 63 EELHAALWRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTI 122 ELH AL RQL FSLAVLAVEIPLGILLALSMPA+G K+SAVLVV+ALSLLIPWNVVGTI Sbjct: 62 GELHDALLRQLGFSLAVLAVEIPLGILLALSMPAKGVKASAVLVVIALSLLIPWNVVGTI 121 Query: 123 WQIYGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIP 182 WQI+GR DIGL+G L MG Y+YTG+A AW TVL+MDVWHWTPLVALL +AGLR+IP Sbjct: 122 WQIFGRTDIGLLGAALAGMGFAYNYTGSAVDAWFTVLVMDVWHWTPLVALLCYAGLRAIP 181 Query: 183 DAYYQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNAT 242 DAYYQAA+IDGAS+ AVFRYIQLPK+RGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNAT Sbjct: 182 DAYYQAAQIDGASRLAVFRYIQLPKLRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNAT 241 Query: 243 TFLSQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILYNWMQRVGTVSDE 293 TFLSQYLT KAVGQFDLGPAAAFS++YF IILL+CFILYNWMQR GT E Sbjct: 242 TFLSQYLTQKAVGQFDLGPAAAFSIVYFLIILLMCFILYNWMQRAGTAGSE 292 Lambda K H 0.328 0.140 0.439 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: 358 Number of extensions: 7 Number of successful extensions: 1 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: 298 Length of database: 297 Length adjustment: 26 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 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 (21.8 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