Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 220 bits (561), Expect = 5e-62 Identities = 118/289 (40%), Positives = 173/289 (59%), Gaps = 2/289 (0%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 L+ + K +G + DL I+ GE V +GPSGCGK+T+LRMIAGLE T GD++I G Sbjct: 47 LQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGR 106 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 R+ND P KR + M+FQ+YAL+PH T+++N+AFG++ S+EE+ +V A +M++L Sbjct: 107 RINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPG 166 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 R LSGGQ+QR+A+ RAI P V L DEPLS LD LR R+EI + ++++ Sbjct: 167 VEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNL 226 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245 TT ++VTHDQ EA++++++IVV+ G +Q G P ++Y+ P N FVA F+G Sbjct: 227 TT-LFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGHANFFDARV 285 Query: 246 TITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEAD 294 Q V +A G T D G+ +R + + VT D Sbjct: 286 LEVLDNDQVRVRIAEGLEFTAD-HVGRWRQGQDVHLVMRAQKINVTSPD 333 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: 330 Number of extensions: 13 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: 406 Length adjustment: 30 Effective length of query: 332 Effective length of database: 376 Effective search space: 124832 Effective search space used: 124832 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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