Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 699 bits (1803), Expect = 0.0 Identities = 355/355 (100%), Positives = 355/355 (100%) Query: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP Sbjct: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 Query: 61 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID Sbjct: 61 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE Sbjct: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG Sbjct: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 Query: 241 SPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVE 300 SPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVE Sbjct: 241 SPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVE 300 Query: 301 PTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERLVA 355 PTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERLVA Sbjct: 301 PTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERLVA 355 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: 576 Number of extensions: 6 Number of successful extensions: 1 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: 355 Length adjustment: 29 Effective length of query: 326 Effective length of database: 326 Effective search space: 106276 Effective search space used: 106276 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: 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