Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101443030.1 BD749_RS03795 ATP-binding cassette domain-containing protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_002846395.1:WP_101443030.1 Length = 259 Score = 140 bits (352), Expect = 5e-38 Identities = 79/230 (34%), Positives = 131/230 (56%), Gaps = 11/230 (4%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 + I G+ K F EVL+ VD+ + GE L+++G SG GKS L+ II+GL + EG Sbjct: 17 ISIRGLKKAFD----DFEVLKGVDLDLFKGENLVVLGRSGTGKSVLIKIISGLLQADEGS 72 Query: 65 IRIGGKNVVGMPPRDRD-----IAMVFQSYALYPTLSVADNIGFAL--EMRKMPKPERQK 117 + + G+ V + PR+ D I FQ+ ALY +++V +N+ F L + M + ER+ Sbjct: 73 VNVLGREVGALKPRELDALRLKIGFSFQNSALYDSMTVRENLEFPLIRHAKHMTEAERED 132 Query: 118 RIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEM 177 I V + + +++ PS+LSGGQR+R+ + R L +P + L+DEP + LD +E+ Sbjct: 133 TIQYVLEAVGLLQAINQMPSELSGGQRKRIGIARTLILKPDIMLYDEPTAGLDPITCIEI 192 Query: 178 RAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIY 227 + I + + +S+ +THD A +G RI ++ G Q+ GT DE++ Sbjct: 193 NSLINEVQEKFNTSSIIITHDLTCARAVGDRIVMLLDGQFQREGTFDEVF 242 Lambda K H 0.318 0.135 0.388 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: 180 Number of extensions: 8 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: 355 Length of database: 259 Length adjustment: 27 Effective length of query: 328 Effective length of database: 232 Effective search space: 76096 Effective search space used: 76096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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