Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 217 bits (553), Expect = 4e-61 Identities = 108/232 (46%), Positives = 149/232 (64%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 +++ + KRF + + + ++E G F +GPSGCGK+TLLR+IAG E G I I Sbjct: 29 LSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIAIR 88 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 GRD + P +R + ++FQ AL+P M+V +N+AF L+ M EI RRV + + + L Sbjct: 89 GRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERVGL 148 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 Y + P QLSGGQ+QRVAI R +V EPA L DEPL LD LR M++E+ L + Sbjct: 149 PGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQAEV 208 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIG 235 TT +Y+THDQ EA+ M+D + V+NAGR EQV +P LYR PA+ FVAGF+G Sbjct: 209 GTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVG 260 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: 377 Number of extensions: 16 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: 418 Length adjustment: 30 Effective length of query: 302 Effective length of database: 388 Effective search space: 117176 Effective search space used: 117176 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