Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 139 bits (350), Expect = 6e-38 Identities = 78/216 (36%), Positives = 131/216 (60%), Gaps = 7/216 (3%) Query: 4 ITLRNVQKRF--GEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIM 61 I ++N++K + G + + ++DL+IE GE V +GPSG GKSTLL +I GL+ ++GQI Sbjct: 7 IKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQIS 66 Query: 62 IDG---RDATEMPPAKRG-LAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNA 117 + G D +++ + + VFQ + L P++TV +N+ PL ++ +++E R Sbjct: 67 VAGVNLMDNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQIPLLGTDIDDKKMEERALKL 126 Query: 118 AKILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEIT 177 K +NL N +D++P +LSGG+RQRVAI RA+V P+ L DEP LD+ + + + Sbjct: 127 LKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVILKLLL 186 Query: 178 ELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIE 213 ++H+ T+I VTH+ A AD+ + + G+I+ Sbjct: 187 DIHKKENVTLIMVTHEPYVA-KQADRSIYVLDGKIK 221 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: 177 Number of extensions: 8 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: 223 Length adjustment: 25 Effective length of query: 307 Effective length of database: 198 Effective search space: 60786 Effective search space used: 60786 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: 47 (22.7 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