Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_057508082.1 ABB28_RS07720 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_001431535.1:WP_057508082.1 Length = 238 Score = 127 bits (319), Expect = 3e-34 Identities = 80/228 (35%), Positives = 120/228 (52%), Gaps = 13/228 (5%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 L++ + K F LR +D+ V GEF+ + GPSG GK+T LNI L+ T G Sbjct: 2 LEMRAVAKVFRTEQVETHALRSLDLLVNEGEFVAVTGPSGSGKTTFLNIAGLLETFTSGT 61 Query: 65 IRIGGKNVVGMPP------RDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118 + G++V + R++ I +FQ + L P L++ DN+ L R M ER++R Sbjct: 62 YLLDGQDVSTLGDDARSRLRNQKIGFIFQGFNLIPDLNLFDNVDVPLRYRGMSAAERRER 121 Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLR---V 175 I++ + + + + PS+LSGGQ+QR A+ RALA P+L L DEP NLD+ + + Sbjct: 122 IEKALSQVGLGSRMKHYPSELSGGQQQRAAIARALAGSPRLLLADEPTGNLDSTMARGVM 181 Query: 176 EMRAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTP 223 E+ EI A+G T V VTHD A + ++ G V L P Sbjct: 182 ELLEEI----NAAGTTIVMVTHDPELAARAQRNVHIVDGQVTDLLREP 225 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: 194 Number of extensions: 10 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: 238 Length adjustment: 26 Effective length of query: 329 Effective length of database: 212 Effective search space: 69748 Effective search space used: 69748 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