Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate HSERO_RS04855 HSERO_RS04855 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >FitnessBrowser__HerbieS:HSERO_RS04855 Length = 296 Score = 467 bits (1201), Expect = e-136 Identities = 232/294 (78%), Positives = 256/294 (87%), Gaps = 1/294 (0%) Query: 6 KPVNQKAWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVFVGTEWFAAVMRDEEL 65 KP N KAWF ILPV + VAFSAI+PLMTVVNYSVQDIISPE++VFVG +WF VMRD EL Sbjct: 3 KPYNNKAWFFILPVFLTVAFSAIIPLMTVVNYSVQDIISPEQKVFVGLDWFREVMRDGEL 62 Query: 66 HAALWRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQI 125 HAAL RQL FS VL V+IPLGI LAL+MP +GWKSSA LV++A+ LLIPWNVVGTIWQI Sbjct: 63 HAALLRQLIFSFCVLLVQIPLGIGLALAMPHKGWKSSATLVILAMPLLIPWNVVGTIWQI 122 Query: 126 YGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY 185 +GRADIGL G +L +GI+Y+Y N AWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY Sbjct: 123 FGRADIGLGGYVLNLLGIDYNYASNPLDAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY 182 Query: 186 YQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFL 245 YQAA+IDGAS++AVFRYIQLPKMRGVL+IAVLLRFMDSFMIYTEPFVLTGGGPGN+TTFL Sbjct: 183 YQAAQIDGASRWAVFRYIQLPKMRGVLVIAVLLRFMDSFMIYTEPFVLTGGGPGNSTTFL 242 Query: 246 SQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILYNWMQRVGTVSDEGAG-HE 298 SQYLT KAVGQFDLGPAAAFSLIYF IILLL F+LYNWMQ G ++ G HE Sbjct: 243 SQYLTQKAVGQFDLGPAAAFSLIYFLIILLLSFVLYNWMQSAGNHANASGGQHE 296 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: 350 Number of extensions: 10 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: 296 Length adjustment: 26 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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