Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate BPHYT_RS33290 BPHYT_RS33290 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >FitnessBrowser__BFirm:BPHYT_RS33290 Length = 298 Score = 463 bits (1192), Expect = e-135 Identities = 222/293 (75%), Positives = 254/293 (86%) Query: 6 KPVNQKAWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVFVGTEWFAAVMRDEEL 65 KPVNQKAW L++PV ICVAFSAILPLMTVVNYSVQDIISP + VFVGTEWF A++ D++L Sbjct: 3 KPVNQKAWLLVVPVFICVAFSAILPLMTVVNYSVQDIISPTQHVFVGTEWFRAIINDDDL 62 Query: 66 HAALWRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQI 125 AL RQ+ FS VL EIPLG+ LAL+MPA GW++SA LVV+A+ LLIPWNVVGTIWQI Sbjct: 63 RGALGRQIIFSACVLLFEIPLGVGLALAMPASGWRASASLVVLAMPLLIPWNVVGTIWQI 122 Query: 126 YGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY 185 +GR DIGL+G L G+EY+YT + AW+TVL+MD+WHWTPLVALL +AGLR+IPDA+ Sbjct: 123 FGRPDIGLLGYALNHAGVEYNYTASPAAAWITVLVMDIWHWTPLVALLCYAGLRAIPDAF 182 Query: 186 YQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFL 245 YQAA IDGAS+FAVFRYI+LPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPG++TTFL Sbjct: 183 YQAAEIDGASRFAVFRYIELPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGDSTTFL 242 Query: 246 SQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILYNWMQRVGTVSDEGAGHE 298 SQYLT KAVGQFDLGPAAAFSLIYF IILLLCFILYNWM+RVG +G + Sbjct: 243 SQYLTQKAVGQFDLGPAAAFSLIYFLIILLLCFILYNWMERVGKGGPASSGED 295 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: 339 Number of extensions: 3 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: 298 Length adjustment: 27 Effective length of query: 271 Effective length of database: 271 Effective search space: 73441 Effective search space used: 73441 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