Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= TCDB::P54933 (332 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 114 bits (285), Expect = 2e-30 Identities = 70/216 (32%), Positives = 112/216 (51%), Gaps = 11/216 (5%) Query: 7 RNVQKRF----GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMI 62 RN+ K + E V+ + L + E V VG SG GKSTLL L+ GL+ +DG++++ Sbjct: 9 RNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLL 68 Query: 63 DGRDATEMPPAKRG------LAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSN 116 G+ +++ A RG + V+Q + L P +T ++N+ PL + + + Sbjct: 69 LGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALA 128 Query: 117 AAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEI 176 + L+ +P +LSGG+RQRVA+ RA+V EP L DEP NLD+ + + Sbjct: 129 LLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLM 188 Query: 177 TELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRI 212 +L+Q T ++ VTHD V D+ + L G I Sbjct: 189 DDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223 Lambda K H 0.320 0.137 0.400 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: 4 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: 332 Length of database: 227 Length adjustment: 25 Effective length of query: 307 Effective length of database: 202 Effective search space: 62014 Effective search space used: 62014 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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