Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 288 bits (736), Expect = 2e-82 Identities = 161/341 (47%), Positives = 216/341 (63%), Gaps = 19/341 (5%) Query: 3 KITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMI 62 +I +R+V+K +G + + +E+G+ +V +GPSGCGK+TLLRLIAGLE V+ G I I Sbjct: 2 QIEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61 Query: 63 DGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILN 122 G D T +PP KR ++MVFQSYAL+PH+ V++NI F L++ K+ EIERR+ +L Sbjct: 62 AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLG 121 Query: 123 LTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQS 182 L+ LD +PG+LSGG +QRVA+GRAI+ E L DEPLSNLDA LR +MR EI L + Sbjct: 122 LSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRR 181 Query: 183 LETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMNLI 242 L TMIYVTHDQVEAMTMAD+IV++ G+I Q SP Y PAN FVA FIG+P MN++ Sbjct: 182 LGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV 241 Query: 243 -----EGPEAAKHGATTI-----------GIRPEHIDLSREAGAWEGEVGVSEHLGSDTF 286 +G A + G + GIRPE++ L+ E+G V E+LGSDTF Sbjct: 242 PLCPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLA-ESGQ-PAMVTGREYLGSDTF 299 Query: 287 LHVHVAGMPTLTVRTGGEFGVHHGDRVWLTPQADKIHRFGA 327 + + G + VRT G + G V LT ++ F A Sbjct: 300 VSCEIHGQEVI-VRTRGRRNIREGTVVHLTWDPGDVNLFDA 339 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: 380 Number of extensions: 18 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: 365 Length adjustment: 29 Effective length of query: 303 Effective length of database: 336 Effective search space: 101808 Effective search space used: 101808 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