Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_047005877.1 AAW01_RS03230 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_001010925.1:WP_047005877.1 Length = 226 Score = 130 bits (327), Expect = 3e-35 Identities = 75/220 (34%), Positives = 118/220 (53%), Gaps = 7/220 (3%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 + + + + F +GD ++VLR VD+ V PGE + L+G SG GKST+L + L+ G Sbjct: 8 VSLRNLTRSFQQGDVRIDVLRGVDLDVGPGEIVALLGQSGSGKSTMLQAVGLLEGGFGGS 67 Query: 65 IRIGGKNVVGMPPRDRD------IAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118 IRI GK + +R + V+Q + L P + +N+ + + E + R Sbjct: 68 IRIAGKEASQLDAAERTSLRREHLGFVYQFHHLLPDFTAQENVVLPQLLLGTKRAEAELR 127 Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178 E+ L + H L RPS+LSGG++QRVA+ RALA +PQL L DEP NLD K + Sbjct: 128 AQELLGSLGLEHRLTHRPSKLSGGEQQRVAVARALANKPQLVLADEPTGNLDEKTSERVL 187 Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQ 218 +E L + G ++ TH++ A + R+ + GV++ Sbjct: 188 SEFLELVRGQGSAALVATHNERLAARM-DRVVRLHDGVIE 226 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: 187 Number of extensions: 7 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: 355 Length of database: 226 Length adjustment: 26 Effective length of query: 329 Effective length of database: 200 Effective search space: 65800 Effective search space used: 65800 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: 47 (22.7 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