Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_000182725.1:WP_008509836.1 Length = 333 Score = 380 bits (976), Expect = e-110 Identities = 193/333 (57%), Positives = 245/333 (73%), Gaps = 1/333 (0%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 M ++ LR+V+K FG VI +D+DI GEF+VFVGPSGCGKSTLLRLIAGLE+++ G + Sbjct: 1 MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 I+G P++RG+AMVFQSYALYPHMTV +N+AF +++A QE + R+ AA++ Sbjct: 61 SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 L LT YL+R P QLSGGQRQRVAIGRAIVR+P FLFDEPLSNLDAALRV RLEI LH Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180 Query: 181 QSLE-TTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKM 239 QS+E TTMIYVTHDQVEAMT+AD+I VL GR+EQ+G+PL LY P +LFVAGFIGSPKM Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240 Query: 240 NLIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLTV 299 N + GP A GA T+G+R EH+ + E G W G+V +E LGSDT++++ + L V Sbjct: 241 NFLTGPHAEPFGAHTVGLRSEHLAIVPERGHWSGQVVHTEILGSDTYVYIDLGLEEPLVV 300 Query: 300 RTGGEFGVHHGDRVWLTPQADKIHRFGADGKAL 332 R G G+ + ++P D +HRF G+A+ Sbjct: 301 RESGVSARKPGEALSISPTGDHVHRFDEKGRAV 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: 353 Number of extensions: 15 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: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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 24 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