Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= TCDB::P54933 (332 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 257 bits (657), Expect = 3e-73 Identities = 143/340 (42%), Positives = 202/340 (59%), Gaps = 14/340 (4%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 M + L + KR+G + + DL +E GEFV +GPSGCGK+T L++IAG DVS GQI Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 ++DGRD T PA RGL +VFQSYAL+PHM+V+ N+AF L+M K+ EI +V ++ Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 + L + DR P +LSGGQRQRVA+ RA+V EP L DEPLSNLDA LR M+ EI + Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 ++ T + VTHDQ EA++++D++VV+ AGR+ Q+ +P LY +P F++ F+G K N Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVG--KAN 238 Query: 241 LIEGP----------EAAKHGATTIGIRPEHIDL-SREAGAWEGEVGVSEHLGSDTFLHV 289 L+ G + G T+ +RPE I L +G +G+V S GS + Sbjct: 239 LLPGDYDLLGSPQVRHESGDGELTLSLRPEKIQLVDAGSGRLQGKVLDSYFFGSQWLYRI 298 Query: 290 HVA-GMPTLTVRTGGEFGVHHGDRVWLTPQADKIHRFGAD 328 H + G T+ G + +G V L QA + D Sbjct: 299 HTSLGEITVVRSNDGSAPLGYGAAVGLDWQASLLRVLAKD 338 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: 319 Number of extensions: 9 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: 342 Length adjustment: 28 Effective length of query: 304 Effective length of database: 314 Effective search space: 95456 Effective search space used: 95456 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