Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011384263.1 AMB_RS09395 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000009985.1:WP_011384263.1 Length = 273 Score = 143 bits (361), Expect = 5e-39 Identities = 82/199 (41%), Positives = 116/199 (58%), Gaps = 4/199 (2%) Query: 12 SYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVP 71 S+GA + L+I+ GEFV +GPSGCGKST L +AG G + +DG V Sbjct: 25 SFGAHAAVEDFSLEIEPGEFVCLLGPSGCGKSTALNAVAGFLRPARGRVAVDGVEVTGPG 84 Query: 72 PSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLP 131 P + MVFQ ++L+P TV +N+AFG R+ +++ E R D++ L R P Sbjct: 85 PER---GMVFQQHSLFPWKTVLENVAFGPRMQGKTRAEARDLAREYLDLVGLGGSAQRYP 141 Query: 132 KALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYV 191 ALSGG QRV I RA+ +P V L DEP LDA R + + +L ++ + T+++V Sbjct: 142 AALSGGMAQRVGIARALVNHPSVLLMDEPFGALDAQTRSIMQESLLRLWGQIGN-TVLFV 200 Query: 192 THDQVEAMTLADRIVVLSA 210 THD EA+ LADR+VV+SA Sbjct: 201 THDIDEALFLADRVVVMSA 219 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: 233 Number of extensions: 11 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: 273 Length adjustment: 27 Effective length of query: 335 Effective length of database: 246 Effective search space: 82410 Effective search space used: 82410 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: 48 (23.1 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