Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >FitnessBrowser__WCS417:GFF1168 Length = 344 Score = 237 bits (605), Expect = 3e-67 Identities = 134/321 (41%), Positives = 182/321 (56%), Gaps = 13/321 (4%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 + +V ++FGE + + +DI+DGEF +GPSG GK+T LRLIAG E S G I I Sbjct: 5 VQFTHVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIH 64 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 G +A +PP +R + VFQ YAL+PHM V+ N+A+ L++ + E R A ++ L Sbjct: 65 GEEAAGLPPYQRDVNTVFQDYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVAL 124 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 Y DR+P QLSGGQRQRVA+ RA+V P L DEPL LD LR M+ E+ +L + L Sbjct: 125 GGYGDRKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQL 184 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIE 243 T I+VTHDQ EA++M+D++ V N GRIEQV +P LY PA FVA F+G+ N+I Sbjct: 185 GITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGT--SNVIR 242 Query: 244 GPEAAKHGATT--IGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPT---LT 298 G A + G T IRPEH+ + EG +G E S + G T L Sbjct: 243 GELAQRLGGTAQPFSIRPEHVRFA------EGPLGTGEVEISGLLHDIQYQGSATRYELK 296 Query: 299 VRTGGEFGVHHGDRVWLTPQA 319 + G + + WL A Sbjct: 297 LENGQALNISRANNQWLDTTA 317 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: 298 Number of extensions: 9 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: 344 Length adjustment: 28 Effective length of query: 304 Effective length of database: 316 Effective search space: 96064 Effective search space used: 96064 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