Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= TCDB::P54933 (332 letters) >MicrobesOnline__882:206675 Length = 247 Score = 158 bits (400), Expect = 1e-43 Identities = 90/227 (39%), Positives = 136/227 (59%), Gaps = 6/227 (2%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 I++RNV K FGE + + LD++ GE VV +GPSG GKSTLLR I LE+V G I++D Sbjct: 9 ISIRNVWKFFGELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIVD 68 Query: 64 GRDA----TEMPPAKRGLAMVFQSYALYPHMTVKKNIAF-PLRMAKMEPQEIERRVSNAA 118 G+D +++ ++ L MVFQS+ L+PH TV +N+ P+R+ K+ E E R + Sbjct: 69 GKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAESRALDLL 128 Query: 119 KILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITE 178 K + +++ + P LSGGQ+QRVAI RA+ P LFDEP S LD + + L++ Sbjct: 129 KKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM-IGEVLDVMV 187 Query: 179 LHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNP 225 TM+ VTH+ A +AD+I+ ++ G+I + G+P + P Sbjct: 188 TLAKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAP 234 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: 211 Number of extensions: 10 Number of successful extensions: 4 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: 247 Length adjustment: 26 Effective length of query: 306 Effective length of database: 221 Effective search space: 67626 Effective search space used: 67626 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: 47 (22.7 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