Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_009120430.1 BUB52_RS15225 polyamine ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_900129655.1:WP_009120430.1 Length = 465 Score = 245 bits (625), Expect = 2e-69 Identities = 119/241 (49%), Positives = 169/241 (70%), Gaps = 2/241 (0%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 I++ +V K FG+ V+ ++L + GEFV +GPSGCGK+TLLRLIAG + S+G I I Sbjct: 8 ISVEHVSKFFGDKAVLNDVNLSVRKGEFVTILGPSGCGKTTLLRLIAGFQTASEGVITIA 67 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 G+D T+ PP +R + VFQ YAL+PH+ V NIAF L++ K+ IE++V A +++ + Sbjct: 68 GKDITQTPPHRRPVNTVFQKYALFPHLNVFNNIAFGLKLKKLPAATIEKKVKQALRMVGM 127 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 T+Y DR LSGGQ+QRVAI RAIV EP L DEPL+ LD +R +M++E+ E+HQ L Sbjct: 128 TDYEDRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHQKL 187 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243 T +YVTHDQ EA+T++D IVV++ G+I+Q G+P+ +Y P N FVA FIG + N++ Sbjct: 188 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQTGTPIDIYNEPINSFVADFIG--ESNILN 245 Query: 244 G 244 G Sbjct: 246 G 246 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: 361 Number of extensions: 7 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: 465 Length adjustment: 31 Effective length of query: 301 Effective length of database: 434 Effective search space: 130634 Effective search space used: 130634 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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