Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= TCDB::P54933 (332 letters) >MicrobesOnline__882:208681 Length = 349 Score = 284 bits (727), Expect = 2e-81 Identities = 158/343 (46%), Positives = 214/343 (62%), Gaps = 19/343 (5%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 M I L V + +G+ + + ++E G+ +V +GPSGCGKST LRLIAGLE V+ G+I Sbjct: 1 MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 +I GRD T +PPA+R LAMVFQSYAL+PH+TV+ NI F L + K+ E ++R+ A +I Sbjct: 61 LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 L L L+R+PG+LSGGQ+QRVA+GRA+V E A L DEPLSNLDA LR MR EI L Sbjct: 121 LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 Q+L TM+YVTHDQ EAM+MAD+I+++ GRI Q +P +Y PA F FIG+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN 240 Query: 241 LI--EGPE------AAKHGATT--------IGIRPEHIDLSREAGAWEGEVGVSEHLGSD 284 L+ +G + ++ G T +GIRPEHI + + W V E+LGS+ Sbjct: 241 LVRLQGNDDGIRVAGSRSGRVTCHAGADCMLGIRPEHIRIVDD--GWRAVVESVEYLGSN 298 Query: 285 TFLHVHVAGMPTLTVRTGGEFGVHHGDRVWLTPQADKIHRFGA 327 + L V G L+V G G ++L + +H F A Sbjct: 299 SVLSCRV-GSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDA 340 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: 334 Number of extensions: 16 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: 349 Length adjustment: 28 Effective length of query: 304 Effective length of database: 321 Effective search space: 97584 Effective search space used: 97584 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