Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 148 bits (374), Expect = 2e-40 Identities = 78/241 (32%), Positives = 133/241 (55%), Gaps = 9/241 (3%) Query: 1 MGKITLRNVQKRFGEA--VVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDG 58 M + L + K+F + + + ++IE+G VG +G GK+TLL+LIAGLE G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 59 QIMIDGRDATE----MPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRV 114 +I+ G+ +P +R + ++FQ YAL+P MT+ +N+ L ++I Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQI---A 117 Query: 115 SNAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRL 174 ++ + L + P QLS GQRQR A+ RA+ P L D+P +LD + + Sbjct: 118 MDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISE 177 Query: 175 EITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFI 234 +I ++ ++ T I +H +A+++AD I +L+ G ++QVG+P+ +Y+ PAN +VA F Sbjct: 178 DIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFF 237 Query: 235 G 235 G Sbjct: 238 G 238 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: 257 Number of extensions: 12 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: 332 Length of database: 345 Length adjustment: 28 Effective length of query: 304 Effective length of database: 317 Effective search space: 96368 Effective search space used: 96368 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 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