Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 343 bits (879), Expect = 5e-99 Identities = 179/361 (49%), Positives = 242/361 (67%), Gaps = 23/361 (6%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 MA I+ID + K +G+ + L I+L+I DGEFV F+GPSGCGKSTLLR++AGLE + G I Sbjct: 1 MATIRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSI 60 Query: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 +G RD+T + A RD+AMVFQ+YALYPHM VR+N+ FG+ +NG + + R+ AA + Sbjct: 61 RLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALNGMKRNEIDRRVNNAAEI 120 Query: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 L++ + LDRKP QLSGGQRQRVAIGRAIV+ P +FL DEPLSNLDA LRV MRVEL LH Sbjct: 121 LRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAALH 180 Query: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 ++LG TMIYVTHDQVEAMT++D++VVL++GR+ Q G+P++L+++P + FVA FIGSP MN Sbjct: 181 ERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRMN 240 Query: 241 VFSSDVGLQ--------------DISLDASAA---------FVGCRPEHIEIVPDGDGHI 277 + V Q ++LD ++ +G RP+ +E+ + H+ Sbjct: 241 FLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTSPEEAHL 300 Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRA 337 A TV + ERLG ES +++ ++GGG + A V G V LR H FD G A Sbjct: 301 AGTVRLVERLGTESHVHIRVEGGGDLTAVVRGTHPVASRDQVHLRLPPEHCHLFDAEGTA 360 Query: 338 I 338 I Sbjct: 361 I 361 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: 400 Number of extensions: 24 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: 391 Length adjustment: 29 Effective length of query: 309 Effective length of database: 362 Effective search space: 111858 Effective search space used: 111858 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