Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 284 bits (726), Expect = 3e-81 Identities = 159/353 (45%), Positives = 217/353 (61%), Gaps = 15/353 (4%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 ++D+RK YG V + G+ ++EG+ +V +GPSGCGK+TLLR+IAGLE +T G + I G Sbjct: 5 IRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIAGT 64 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTP 125 V +PP KR I+MVFQSYAL+PH+ V +N+ FG+++ + +EI+RR++ D+L L+ Sbjct: 65 DVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGLSG 124 Query: 126 YLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSD 185 LD P LSGG +QRVA+GRAI V L DEPLSNLDA LR + R EI L R+ Sbjct: 125 RLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRLG- 183 Query: 186 TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPA 245 TMIYVTHDQVEAMT+ADRIV++ G I Q +P YERPAN FVARFIG+P MN++P Sbjct: 184 ITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVPL 243 Query: 246 TITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIV 305 T G A GG+ + + + FG+RPE+LR+ E+ V+ Sbjct: 244 CPTQGG---AALEPGGRLLFPGMDPD------RYLFGIRPENLRLAESGQ---PAMVTGR 291 Query: 306 EALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQ 358 E LG T + E + + +I + G + G V T D ++LFD Q Sbjct: 292 EYLGSDTFVSCE--IHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQ 342 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: 361 Number of extensions: 15 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: 365 Length adjustment: 29 Effective length of query: 333 Effective length of database: 336 Effective search space: 111888 Effective search space used: 111888 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