Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 165 bits (417), Expect = 2e-45 Identities = 108/330 (32%), Positives = 181/330 (54%), Gaps = 17/330 (5%) Query: 1 MGKITLRNVQKRFGE-AVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQ 59 M + + V KR+ ++ + L ++ G V VG SG GKS+LLR+IAGLE S G Sbjct: 1 MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60 Query: 60 IMIDGRD----ATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVS 115 + + + A ++ P + ++ Q Y LYP+ TV++NIA PL + Q+ R + Sbjct: 61 VHLGDQKILNPAQKLVPGYDEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQK--ERTA 118 Query: 116 NAAKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLE 175 ++L+L + D++P QLSGGQ+Q+VAIGRA+ EP L DEP S+LDA + ++ E Sbjct: 119 EILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEE 178 Query: 176 ITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIG 235 + E+ +LE T+I+VTHD +A+ M+++++++ G++ Q G+ ++R PA+ +VA G Sbjct: 179 LKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 Query: 236 SPKMNLIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMP 295 +NLI G E A +RP + ++ + + EV + L L V + Sbjct: 239 --YLNLIPGAEEAY-------VRPSEVKITSKTSI-KAEVVKQQFLIHYNLLTVKLEDSE 288 Query: 296 TLTVRTGGEFGVHHGDRVWLTPQADKIHRF 325 V+ GD V+L Q +++ +F Sbjct: 289 LFWKVDDPSRSVNVGDEVFLDYQKEQLIQF 318 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: 185 Number of extensions: 9 Number of successful extensions: 3 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: 318 Length adjustment: 28 Effective length of query: 304 Effective length of database: 290 Effective search space: 88160 Effective search space used: 88160 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: 48 (23.1 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