Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 270 bits (690), Expect = 4e-77 Identities = 144/295 (48%), Positives = 194/295 (65%), Gaps = 14/295 (4%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 M + R++ KRF + +DL + + EF+V +GPSG GK+TLLRLIAGLE + G I Sbjct: 1 MATVETRSLTKRFDGTNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 ++ GR T +PP +AMVFQSYALYPH++V NIAFPL +M + I R+VS AA + Sbjct: 61 LVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAAL 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 + + L R+P QLSGG+RQRVA+ RA+VREP AFL DEPLSNLDA LR + R E+ +L Sbjct: 121 FGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQ 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 + L TT IYVTHDQ+EA+ + D++ +L+ GR+ Q+G+P +Y PA+ FVA FIGSP MN Sbjct: 181 RRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPPMN 240 Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREA-GAWEG------EVGVSEHLGSDTFLH 288 L++ A G RPEH L RE G+ E + E+LGSD ++ Sbjct: 241 LVD------TDALVTGFRPEHF-LPREVYGSDEALEPFPFHITRIENLGSDRLVY 288 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: 327 Number of extensions: 11 Number of successful extensions: 1 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: 351 Length adjustment: 29 Effective length of query: 303 Effective length of database: 322 Effective search space: 97566 Effective search space used: 97566 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