Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 235 bits (600), Expect = 1e-66 Identities = 139/328 (42%), Positives = 194/328 (59%), Gaps = 28/328 (8%) Query: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 + I I+K + T A+ ++NLDI GE +G SG GKSTLLR LAG E ++G I + Sbjct: 15 LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74 Query: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123 G+DVT + P R M+FQSYAL+PHMTV +N+ G+K + ++R+A +++++ Sbjct: 75 GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134 Query: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183 E Y RKP QLSGGQ+QRVA+ R++ K P + L DEP+ LD KLR +M++EL + + + Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194 Query: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVF- 242 GAT + VTHDQ EAMTMA +I ++ +GRI Q+GSP+D+Y PNSR AEFIGS +N+F Sbjct: 195 GATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGS--VNIFE 252 Query: 243 -------SSDVGLQDISLDA--------------SAAFVGCRPEHIEIVPD-GDGH---I 277 + V L LDA +A V RPE I + PD DG Sbjct: 253 AHIREDEADSVTLTSDLLDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPDGENNWS 312 Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVA 305 TV LG + Y+ L G ++ A Sbjct: 313 CGTVDNIAYLGDITSYYVKLASGKRVQA 340 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: 300 Number of extensions: 11 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: 372 Length adjustment: 29 Effective length of query: 309 Effective length of database: 343 Effective search space: 105987 Effective search space used: 105987 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