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 CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 141 bits (355), Expect = 3e-38 Identities = 83/255 (32%), Positives = 132/255 (51%), Gaps = 5/255 (1%) Query: 4 VTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIR 63 +TF ++ Y PA+ + ++++ GE ++G SG GKST +R++ GLE + G + Sbjct: 2 ITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVI 61 Query: 64 IGDRDVTHLPPKD-----RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEE 118 + DV L R + M+FQ++ L TVA N+ F LK+AG P AE++ + E Sbjct: 62 VDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQNVAFPLKLAGRPAAEVKARTAE 121 Query: 119 AAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQI 178 + + L+ + + P LSGGQ+QRV + RA+ P+V L DE S LD + I Sbjct: 122 LLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPETTEQILDLI 181 Query: 179 ASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGS 238 A L R LG+T V +TH+ + DRVAVL G + + + ++ PA+ F+ Sbjct: 182 AGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASDTARRFVRE 241 Query: 239 PAMNLVEVPITDGGV 253 ++ P G V Sbjct: 242 AEGDVTAAPGVGGRV 256 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: 311 Number of extensions: 12 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: 332 Length adjustment: 29 Effective length of query: 348 Effective length of database: 303 Effective search space: 105444 Effective search space used: 105444 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