Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 191 bits (484), Expect = 3e-53 Identities = 113/345 (32%), Positives = 189/345 (54%), Gaps = 29/345 (8%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 + L +V + GE ++ ++L++++GE+ + +GP+G GK+ +L IAG+ G I Sbjct: 2 LRLEHVTVKLGEFQLL-DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 R+ + P +R + V+Q YAL+PH+TVK+NI F ++ K+ + I+ ++ +L + Sbjct: 61 ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 + L+R P LSGG++QR A+ RA++ P L DEPLS LD + N + E+ ++HQ+L Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243 +TT ++VTHD EAM +ADKI V++ G+I QVG+P ++ P N FVA F+G N+ E Sbjct: 181 KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFE 238 Query: 244 GP----------------EAAKHGATTIGIRPEHIDLSREA------GAWEGEVGVSEHL 281 G K G + + PE I LS+E + G+V + Sbjct: 239 GQVNDDKVSLAPDVDIFVNTGKQGKVKVAVPPEDIALSKEPFDLCYHYQFNGKVLNISNQ 298 Query: 282 GSDTFLHVHVAGMPTL---TVRTGGEFGVHHGDRVWLTPQADKIH 323 G+ + + + + G+P + T R E + GD +W + H Sbjct: 299 GALSKITIDI-GIPLVCFATTRFVKETAITVGDNLWAGFNSSSTH 342 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: 291 Number of extensions: 18 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: 344 Length adjustment: 28 Effective length of query: 304 Effective length of database: 316 Effective search space: 96064 Effective search space used: 96064 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: 49 (23.5 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