Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 206 bits (523), Expect = 1e-57 Identities = 127/349 (36%), Positives = 194/349 (55%), Gaps = 28/349 (8%) Query: 6 IDKINK-FYGTTQALFD-INLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 +D++ K F G++ A D ++ ++E GE + VGPSGCGK+TLLR +AG E + SG I++ Sbjct: 9 LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68 Query: 64 GRDVTTVE----PADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 G V T + P R + MVFQ YAL+PH+TV +N+ FG++ + ++ +A Sbjct: 69 GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVARQALA---- 124 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 ++ LE R P +LSGGQ+QRVA+ RA+ P + L DEPLSNLD ++R+++R EL + Sbjct: 125 LVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDI 184 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGS--- 236 +Q AT I VTHDQ EA+++ D++ V+ GR EQ+G P +L+ P SRFVAEF+ Sbjct: 185 LRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQANF 244 Query: 237 -----------PAMNVFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKE 285 + F + GL+ V R E + + P +G V ++ Sbjct: 245 LATEYQGDAWRTVLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEG--TGLVRDRQ 302 Query: 286 RLGGESLLYLGLKGGGQIVARVGGDDETKVGAA--VSLRFSRHRLHQFD 332 LG + ++ L G +I + VG A V LR + RL+ +D Sbjct: 303 FLGRDYRYFVQLPAGLEIQVLGPVSEAIAVGTAVQVQLRTGQARLYPYD 351 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: 282 Number of extensions: 12 Number of successful extensions: 3 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: 368 Length adjustment: 29 Effective length of query: 309 Effective length of database: 339 Effective search space: 104751 Effective search space used: 104751 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