Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_012102195.1 CKL_RS08845 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000016505.1:WP_012102195.1 Length = 352 Score = 206 bits (523), Expect = 1e-57 Identities = 99/231 (42%), Positives = 153/231 (66%), Gaps = 1/231 (0%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 ++++ K++G+ + I I+ G+ + +GPSG GK+T+LR+IAGLE G+++IDG+ Sbjct: 5 VRNLNKNFGSYEASKNISFGIERGKLIGLLGPSGSGKTTILRIIAGLETADSGEIYIDGK 64 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 VND+ P KRGI VFQ+YAL+ +MTVY N+AFG+ I +E K+ I RV +++ L Sbjct: 65 LVNDISPGKRGIGFVFQNYALFRNMTVYQNIAFGLSIKKEDKKYIKERVTELIELIGLKG 124 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 R P LSGGQ+QRVA RAI P++ L DEP + +DA +R R + ++ ++ Sbjct: 125 LEKRYPSQLSGGQKQRVAFARAIAPKPQLLLLDEPFAAIDAKVRKELRTWLKQMIHKLG- 183 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIG 236 T ++VTHDQ EA+ +AD I++ + G IEQ+G+ +E+Y+ P FVA F+G Sbjct: 184 ITSVFVTHDQEEAVEVADEIIITNLGSIEQIGSAVEIYKNPQTAFVATFVG 234 Lambda K H 0.320 0.137 0.387 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: 278 Number of extensions: 9 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: 362 Length of database: 352 Length adjustment: 29 Effective length of query: 333 Effective length of database: 323 Effective search space: 107559 Effective search space used: 107559 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 24 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