Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 218 bits (556), Expect = 2e-61 Identities = 133/353 (37%), Positives = 203/353 (57%), Gaps = 24/353 (6%) Query: 4 LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63 L ++ I KS+ + ++LDI +GE +G SG GKSTLLRM+AG E G + +D Sbjct: 15 LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74 Query: 64 GERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQL 123 G+ V +PP R M+FQSYAL+PHMTV N+A G++ + K EI RV ++++ Sbjct: 75 GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134 Query: 124 TPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERM 183 PY R P+ LSGGQ+QRVA+ R++ + PK+ L DEP+ LD LR ++E+ ++ E + Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194 Query: 184 SDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVI 243 T + VTHDQ EAMT+A RI +++ G I Q+G+P+++YE P + A FIGS +N+ Sbjct: 195 G-ATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGS--VNIF 251 Query: 244 PATITATGQQTAVSLAGGKSVTLDVP-------TNASENGKTASFGVRPEDLRVT----E 292 A I + +V+L S LD P T +E+ T +RPE + +T + Sbjct: 252 EAHI-REDEADSVTLT---SDLLDAPVFIDRGVTTPAESTATL-VALRPEKIYLTPDKPD 306 Query: 293 ADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGR----GDKV 341 ++ GTV + LG++T Y++ L + + A M + R G GD+V Sbjct: 307 GENNWSCGTVDNIAYLGDITSYYVK-LASGKRVQATMANVERRGERPTWGDRV 358 Lambda K H 0.320 0.137 0.387 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: 332 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: 362 Length of database: 372 Length adjustment: 30 Effective length of query: 332 Effective length of database: 342 Effective search space: 113544 Effective search space used: 113544 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