Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= TCDB::P54933 (332 letters) >MicrobesOnline__882:209027 Length = 368 Score = 246 bits (628), Expect = 6e-70 Identities = 122/248 (49%), Positives = 169/248 (68%), Gaps = 2/248 (0%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 I LR V K F + + ++DL+I +GEF+ +GPSGCGK+T+LRLI+G E G I + Sbjct: 8 IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 G+ + PP R + VFQ+YAL+PHM+V++N+ F LRM + EI RRV +A ++++L Sbjct: 68 GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHL 127 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 + DRRP QLSGGQ+QRVAI RA+V P L DEP S LD LR M+LEI L + L Sbjct: 128 EAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQL 187 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243 T ++VTHDQ EA M+D++VV+N G+IEQ+GSP +Y PANL+VA F+G ++N++ Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVG--EINILN 245 Query: 244 GPEAAKHG 251 AA HG Sbjct: 246 AVIAANHG 253 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: 366 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: 368 Length adjustment: 29 Effective length of query: 303 Effective length of database: 339 Effective search space: 102717 Effective search space used: 102717 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