Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 234 bits (596), Expect = 3e-66 Identities = 145/335 (43%), Positives = 193/335 (57%), Gaps = 23/335 (6%) Query: 4 ITLRNVQKRFGEAVV-IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLE-DVSDGQIM 61 ITLR+ K F + + + LDLDI GE VV +GPSGCGK+T LR+IAGLE + G +M Sbjct: 7 ITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM 66 Query: 62 IDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKIL 121 D T +P +RG+ MVFQSYAL+P+MTV +NIA+ LR+ +++ RRV ++ Sbjct: 67 FGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMM 126 Query: 122 NLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQ 181 +L + +RR QLSGGQRQRVA+ RAI +P L DEPL+ LDA LR +R +I +L + Sbjct: 127 HLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLR 186 Query: 182 SLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGS----- 236 SL T +YVTHDQ EAM + D+I+V++ GRI Q G+P +YR PAN FVA FIG+ Sbjct: 187 SLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGTMNRLP 246 Query: 237 ---------------PKMNLIEGPEAAKHGATTIGIRPEHIDLSR-EAGAWEGEVGVSEH 280 P+ AA + RPE + L++ E G V + Sbjct: 247 AVLEADAWRVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTALF 306 Query: 281 LGSDTFLHVHVAGMPTLTVRTGGEFGVHHGDRVWL 315 LG+ T L V V L V T G GDRV L Sbjct: 307 LGNYTRLLVDVGAPAPLVVDTTRRDGWLAGDRVGL 341 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: 317 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: 357 Length adjustment: 29 Effective length of query: 303 Effective length of database: 328 Effective search space: 99384 Effective search space used: 99384 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