Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 233 bits (595), Expect = 4e-66 Identities = 129/327 (39%), Positives = 194/327 (59%), Gaps = 8/327 (2%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA ++++ ++K YG A+ +L +E GEFV +GPSGCGK+T L+ +AG VS G+I Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 + GRD+T +PA R L +VFQSYAL+PHM+VR+N+ FG+K+ ++ + Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 ++L + DR P +LSGGQRQRVA+ RA+V P V L DEPLSNLDA LR +M+ E+ + Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 +G T + VTHDQ EA++++D++VV+ GR+ Q+ +P LY P +RF+++F+G N Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGK--AN 238 Query: 241 VFSSD---VGLQDISLDA--SAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYL 295 + D +G + ++ + RPE I++V G G + V G + L + Sbjct: 239 LLPGDYDLLGSPQVRHESGDGELTLSLRPEKIQLVDAGSGRLQGKVLDSYFFGSQWLYRI 298 Query: 296 GLKGGGQIVARVG-GDDETKVGAAVSL 321 G V R G GAAV L Sbjct: 299 HTSLGEITVVRSNDGSAPLGYGAAVGL 325 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: 304 Number of extensions: 12 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: 342 Length adjustment: 28 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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