Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate HSERO_RS17020 HSERO_RS17020 sugar ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS17020 Length = 406 Score = 298 bits (764), Expect = 1e-85 Identities = 179/386 (46%), Positives = 235/386 (60%), Gaps = 32/386 (8%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA + + Y G P + LD+ I DGEF+VL+GPSGCGKST LRM+AGLED++GG Sbjct: 1 MADIHCQALAKHYAGGP-PVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 +RIG V LP ++R++AMVFQNYALYPHM+V DN+ F L+ P AEI ++V E A Sbjct: 60 TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +L+L L+RKP+A+SGGQ+QR A+ RAI++ P VFL DEPLSNLDAKLR R I Sbjct: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L +RL TTVYVTHDQ+EAMT+ DRV +++DG + Q SP +Y P NLF AGFIG+PA Sbjct: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDR--------TVTVGVRPEHFDVVELG 292 MN + G V+ + + + A G+R V + VRP+H V + Sbjct: 240 MNFL-----SGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDH---VRIA 291 Query: 293 G--AVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPE 350 G AASL+ VSV +VE LGAD + T G + L V ++P+ Sbjct: 292 GEREPAASLT---------CPVSVELVEILGADALL--TTRCGDQT--LTALVPADRLPQ 338 Query: 351 KGSTLHVVPRPGETHVFSTSTGERLS 376 G+TL + E HVF +GE LS Sbjct: 339 PGATLTLALDQHELHVFDVESGENLS 364 Lambda K H 0.317 0.135 0.379 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: 446 Number of extensions: 14 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: 377 Length of database: 406 Length adjustment: 31 Effective length of query: 346 Effective length of database: 375 Effective search space: 129750 Effective search space used: 129750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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