Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 320 bits (820), Expect = 4e-92 Identities = 174/358 (48%), Positives = 231/358 (64%), Gaps = 21/358 (5%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 M +K+D +NK G + L D++L+I GEFVVFVGPSGCGKSTLLR +AGL+ + +G + Sbjct: 1 MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 I R V +EP +R + MVFQSYALYPHM+V +N+ FG+K+ E +ER+ A++ Sbjct: 61 LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 LQL+ L RKP +LSGGQRQRVA+GRA+ + P + LFDEPLSNLDA LRVQMR E+ LH Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 +LG+TMIYVTHDQVEAMT+ADKIVVLN GR+EQVGSP +LY +P SRFVA F+GSP MN Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 VFSSD--------------VGLQDISLDAS------AAFVGCRPEHIEIVPDGDGHIAAT 280 ++ +G+ + D+S +G RPEH+ + DG + Sbjct: 241 FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLSLGVRPEHVSL-KAADGTVGVI 299 Query: 281 VHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 V E LG E+ ++L ++ R + +VG V L+ LH FD G A+ Sbjct: 300 VTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFDADGTAL 357 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: 391 Number of extensions: 13 Number of successful extensions: 2 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: 381 Length adjustment: 29 Effective length of query: 309 Effective length of database: 352 Effective search space: 108768 Effective search space used: 108768 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