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 RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 227 bits (578), Expect = 4e-64 Identities = 136/322 (42%), Positives = 193/322 (59%), Gaps = 20/322 (6%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVN-GGAIRIGDRDVTHLPPKDRD 78 A+ LD+ I GE +VL+GPSGCGK+T+LR++AGLE + GG + GD DVT LP + R Sbjct: 22 ALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGDNDVTPLPIEQRG 81 Query: 79 IAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSG 138 + MVFQ+YAL+P+MTVA+N+ + L++ + A R++V+E ++ L + +R+ LSG Sbjct: 82 VGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQLSG 141 Query: 139 GQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVE 198 GQRQRVA+ RAI +P+V L+DEPL+ LDAKLR + R I L R L IT VYVTHDQ E Sbjct: 142 GQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVTHDQAE 201 Query: 199 AMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNS 258 AM +GDR+ V+ G + Q +P+ +Y PAN FVA FIG+ MN + + + Sbjct: 202 AMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLPAVLEADAWRVPGG 259 Query: 259 VVPVNREALSAADKGDRTVTVGVRPEHFDVVE-----LGGAVAASLSKDS-------ADA 306 +VP + A S A + RPE + + LGG+V +L + A Sbjct: 260 LVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGGSVVTALFLGNYTRLLVDVGA 319 Query: 307 PAGLAVSVNVVEELGADGYVYG 328 PA L VV+ DG++ G Sbjct: 320 PAPL-----VVDTTRRDGWLAG 336 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: 360 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: 377 Length of database: 357 Length adjustment: 30 Effective length of query: 347 Effective length of database: 327 Effective search space: 113469 Effective search space used: 113469 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: 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