Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 3607559 Dshi_0971 ABC transporter related (RefSeq)
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Dino:3607559 Length = 334 Score = 499 bits (1284), Expect = e-146 Identities = 250/330 (75%), Positives = 278/330 (84%), Gaps = 1/330 (0%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 MG+I L V K FG+ VIP LDL IEDGEF VFVGPSGCGKSTLLRLIAGLED++ G I Sbjct: 1 MGQIKLNQVTKSFGDVEVIPPLDLTIEDGEFAVFVGPSGCGKSTLLRLIAGLEDITSGHI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 IDG+DAT +PPAKRGLAMVFQSYALYPHM+V+KNIAFP++MA ++ E +RR+ AAK Sbjct: 61 EIDGKDATNVPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIDEAEQQRRIDAAAKA 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 LNLT+YLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRV MRLEI+ELH Sbjct: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 + LETTMIYVTHDQVEAMTMADKIVVL AG IEQVGSPL LY +P N FVAGFIGSPKMN Sbjct: 181 KRLETTMIYVTHDQVEAMTMADKIVVLRAGHIEQVGSPLELYHSPRNEFVAGFIGSPKMN 240 Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVH-VAGMPTLTV 299 LI+G EAAKHG TIGIRPEH D+S G WEG VGV+EHLGSDTFLH+H V +TV Sbjct: 241 LIKGAEAAKHGVATIGIRPEHTDVSTTEGLWEGRVGVAEHLGSDTFLHIHGVPDCDPMTV 300 Query: 300 RTGGEFGVHHGDRVWLTPQADKIHRFGADG 329 R GE V HGD+++LTPQ DK+H+F A G Sbjct: 301 RVDGELPVKHGDKIFLTPQLDKLHKFDAQG 330 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: 442 Number of extensions: 14 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 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