Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 120 bits (301), Expect = 3e-32 Identities = 64/210 (30%), Positives = 108/210 (51%), Gaps = 7/210 (3%) Query: 9 VQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMIDGRDAT 68 ++K +G ++ ++ +++ GE V +GPSG GKSTLL ++ L+ DG + + G Sbjct: 7 IRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQLKGTVIN 66 Query: 69 EMPP------AKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILN 122 ++ + + VFQ + L P + +NI P +AK ++ E R + Sbjct: 67 KLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFELLDLFG 126 Query: 123 LTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQS 182 L + +P QLSGG++QRVAI RA++ P+ L DEP NLD+ + L + Sbjct: 127 LKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQLFVSLRDN 186 Query: 183 LETTMIYVTHDQVEAMTMADKIVVLNAGRI 212 T + VTH++ A T +D++V + G I Sbjct: 187 FHQTFVIVTHNEHLAKT-SDRVVSMKDGLI 215 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: 144 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: 216 Length adjustment: 25 Effective length of query: 307 Effective length of database: 191 Effective search space: 58637 Effective search space used: 58637 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 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