Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_072908848.1 BUB13_RS11230 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_900142125.1:WP_072908848.1 Length = 361 Score = 204 bits (518), Expect = 4e-57 Identities = 125/318 (39%), Positives = 182/318 (57%), Gaps = 17/318 (5%) Query: 6 LKDIRKSYGA----VDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMF 61 ++D+ ++Y + + + +DL I +GPSGCGK+TLLR I GLE GG+++ Sbjct: 5 IQDLVRTYSSEGKQIKALDHVDLTIPANRIFTLLGPSGCGKTTLLRCIVGLEVPDGGEIY 64 Query: 62 IDGERVND------VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVR 115 I E V VPP +RG+ MVFQ+YA++PHM V+DN+A+ ++ + +KEEI R+V Sbjct: 65 IGDELVWSKEKNIFVPPERRGLGMVFQTYAIWPHMNVFDNVAYPLQTQKMAKEEIRRKVA 124 Query: 116 GAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIE 175 D +QL+ Y +R LSGGQ+QRVA+ RA+ PKV LFDEPLSNLDA LR TR E Sbjct: 125 KVLDFVQLSGYENRPATKLSGGQQQRVALARALVAEPKVILFDEPLSNLDAKLREETRKE 184 Query: 176 IAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFI 235 + + T IYVTHD+VEA+ L+D I V+ +G I ++ P ++Y + FVA FI Sbjct: 185 LRSFLTEL-QITAIYVTHDRVEALALSDLIAVMRSGKIIEINEPKKIYFNSDSQFVADFI 243 Query: 236 GSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVT---E 292 G N+I T+ AV A + + G+ A VRPE +R+ + Sbjct: 244 G--RANLIRGTVEELDGDHAV-FASEIGPVRALNSQQIPLGQEAFLCVRPEFIRLAKERK 300 Query: 293 ADDFLFEGTVSIVEALGE 310 + + G V + +GE Sbjct: 301 EEQNSYSGKVETLIFIGE 318 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: 318 Number of extensions: 17 Number of successful extensions: 3 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: 361 Length adjustment: 29 Effective length of query: 333 Effective length of database: 332 Effective search space: 110556 Effective search space used: 110556 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 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