Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_034411801.1 H566_RS0113525 polyamine ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_000482785.1:WP_034411801.1 Length = 372 Score = 221 bits (563), Expect = 2e-62 Identities = 134/353 (37%), Positives = 191/353 (54%), Gaps = 36/353 (10%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 + + + KRF + + + L I GE +G SGCGKSTLLR++AG E + G I+++ Sbjct: 17 LRIERLTKRFDDVAAVDDVSLSIRKGEIFALLGSSGCGKSTLLRMLAGFEAPTAGHILLE 76 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 RD + +PP +R + M+FQSYAL+PH+TV +NIAF L+ + EI RV ++ L Sbjct: 77 NRDISALPPYERPINMMFQSYALFPHLTVWENIAFGLKRDGLPKTEIAERVEAMLSLVQL 136 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 + R+P QLSGGQ+QRVA+ R++ ++P L DEPL LD LR +LE+ + + + Sbjct: 137 NKFAKRKPHQLSGGQQQRVALARSLAKKPRLLLLDEPLGALDKKLREQTQLELVNIIKQV 196 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGS------- 236 T + VTHDQ EAMTMAD+I +++AG QVG P +Y PAN FVA FIG+ Sbjct: 197 GVTCVMVTHDQEEAMTMADRIAIMSAGSFLQVGQPHEIYETPANRFVADFIGNVNLFDGT 256 Query: 237 -----PKMNLIEGPEA---AKHGAT-------TIGIRPEHIDLSR------EAGAWEGEV 275 P +I P+ HG T T+ +RPE I L R E E V Sbjct: 257 LVVDEPDHVVINTPQCGFYVSHGITGTVGMPVTVALRPEKIALGRDRPDSTEHNCAEVTV 316 Query: 276 GVSEHLGSDT-FLHVHVAGMPTL-----TVRTGGEFGVHHGDRVWLTPQADKI 322 + GS T ++ GM T R G F + GDR+W + A+ + Sbjct: 317 ADYAYFGSFTLYVLAFPGGMKVKVSVANTDRHGEYFAI--GDRLWASWAAEAL 367 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: 306 Number of extensions: 11 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: 372 Length adjustment: 29 Effective length of query: 303 Effective length of database: 343 Effective search space: 103929 Effective search space used: 103929 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 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