Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate PfGW456L13_4204 ABC transporter, ATP-binding protein
Query= TCDB::P54933 (332 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4204 Length = 329 Score = 246 bits (627), Expect = 7e-70 Identities = 133/298 (44%), Positives = 191/298 (64%), Gaps = 7/298 (2%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 M ++++++QK F V ++ +I+ GEFV +GPSGCGKSTLLR IAGL V G+I Sbjct: 1 MSYVSVQHLQKSFAGTTVFSDINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 ++DG D + P KRG+ MVFQSYAL+P+MTV++N+AF LRM K+ + +RV+ K+ Sbjct: 61 LLDGADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSRKRVAEVLKL 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 + L ++ R P QLSGGQ QRVA+ R++V P L DEPLS LDA +R ++R +I ++ Sbjct: 121 VELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQ 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 + L T I+VTHDQ EA+TM+D+I ++N G+I Q G TLY P ++F AGFIG+ N Sbjct: 181 RELGLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGN--YN 238 Query: 241 LIEGPEAAK----HGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGM 294 L++ A+K I IRPE I+LS + G + +V LG+ V G+ Sbjct: 239 LLDADSASKLLQRPINKRIAIRPEAIELSLD-GELDAQVRSHSLLGNVIRYRVEARGV 295 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: 258 Number of extensions: 8 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: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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