Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 204 bits (520), Expect = 2e-57 Identities = 133/363 (36%), Positives = 189/363 (52%), Gaps = 37/363 (10%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA I + I K YG L ++L + GE +GPSGCGK+ LLR +AG E +G I Sbjct: 1 MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60 Query: 61 EIGGRDVTT------VEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERI 114 IGG V+ V P RDL +VFQ YA++PHM+V +N+ + +K+ G R ++ Sbjct: 61 SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120 Query: 115 AEAARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRV 174 E ++ L +R P QLSGGQ+QRVA+ RA+V PS+ L DEPL NLDA LR +MR Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180 Query: 175 ELEGLHKQLGATMIYVTHDQVEAMTMADKIVVLNR-GRIEQVGSPMDLYHKPNSRFVAEF 233 E++ L + LG T++YVTHDQ A+ ++D++ +++ G I QVG+P +++ +P FV F Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240 Query: 234 IG----------SPAMNVFSSDV----GLQDISLDASAAFVGCRPEHIEIVPDGDGHIAA 279 +G AM + GL D DA G RP + + GDG + Sbjct: 241 MGVANFLPARRRGMAMLAAGGEQPVPWGLPD--GDAEHWMAGFRPSDVRLARQGDG-LRG 297 Query: 280 TVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSR--------HRLHQF 331 TV LG + + + G A +T A L F+ H LH F Sbjct: 298 TVRRASFLGAMTDYLIEVDG-----ASFRTQLDTHEALARGLMFAEGEPCVVGFHDLHWF 352 Query: 332 DEA 334 D A Sbjct: 353 DAA 355 Lambda K H 0.320 0.139 0.396 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: 312 Number of extensions: 15 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: 338 Length of database: 366 Length adjustment: 29 Effective length of query: 309 Effective length of database: 337 Effective search space: 104133 Effective search space used: 104133 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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