Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::P54933 (332 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 314 bits (805), Expect = 2e-90 Identities = 180/355 (50%), Positives = 226/355 (63%), Gaps = 39/355 (10%) Query: 14 GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMIDGRDATEMPPA 73 G+ + +LDL+I DGEF+V VGPSGCGKST LR++AGLEDV++G I I RD T +PP Sbjct: 16 GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75 Query: 74 KRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNLTNYLDRRPGQ 133 R +AMVFQ+YALYPHMTV N+ F L++A + EI +V AAKIL+LT +LDR+P Sbjct: 76 DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135 Query: 134 LSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSLETTMIYVTHD 193 LSGGQRQRVA+GRAIVREP FL DEPLSNLDA LRV+ R +I L + L T +YVTHD Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195 Query: 194 QVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLIEGP-------- 245 QVEAMTM D++ VL G ++QV +P +Y PANLFVAGFIGSP MNL+E P Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVKF 255 Query: 246 -------------EAAKHG--ATTIGIRPEHIDLSREAGAWEG---------EVGVSEHL 281 EAA G T+G+RPEH+D+ G EG V V E L Sbjct: 256 GESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDI---VGGTEGGGEDKGLAVTVNVVEEL 312 Query: 282 GSDTFLHVHV-AGMPT--LTVRTGGEFGVHHGDRVWLTPQADKIHRFG-ADGKAL 332 G+D +++ G T L VR GG GD++ + P+A + H F + GK L Sbjct: 313 GADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTSTGKRL 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: 394 Number of extensions: 15 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: 369 Length adjustment: 29 Effective length of query: 303 Effective length of database: 340 Effective search space: 103020 Effective search space used: 103020 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 Apr 09 2024. 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