Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 224 bits (571), Expect = 3e-63 Identities = 125/319 (39%), Positives = 184/319 (57%), Gaps = 30/319 (9%) Query: 4 ITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMID 63 +++R + K F + + +++LDI GE +G SG GKSTLLR++AG E + G IM+D Sbjct: 15 LSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLD 74 Query: 64 GRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNL 123 G+D T +PP R M+FQSYAL+PHMTV++NIA L+ K+ EI RV+ K++ + Sbjct: 75 GQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSEIRDRVAAMLKLVKM 134 Query: 124 TNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSL 183 Y R+P QLSGGQ+QRVA+ R++ + P L DEP+ LD LR M+LE+ E+ +++ Sbjct: 135 EPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENV 194 Query: 184 ETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM---- 239 T + VTHDQ EAMTMA +I ++ GRI Q+GSP+ +Y +P + A FIGS + Sbjct: 195 GATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIGSVNIFEAH 254 Query: 240 -------------NLIEGPEAAKHGATT--------IGIRPEHIDLSREAGAWE-----G 273 +L++ P G TT + +RPE I L+ + E G Sbjct: 255 IREDEADSVTLTSDLLDAPVFIDRGVTTPAESTATLVALRPEKIYLTPDKPDGENNWSCG 314 Query: 274 EVGVSEHLGSDTFLHVHVA 292 V +LG T +V +A Sbjct: 315 TVDNIAYLGDITSYYVKLA 333 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: 295 Number of extensions: 15 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 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