Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 180 bits (457), Expect = 5e-50 Identities = 103/289 (35%), Positives = 168/289 (58%), Gaps = 10/289 (3%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M+ L ++DI G+ + + GIDL ++G++V +GPSG GKS LL I G G + Sbjct: 1 MSFLEVRDIYLDVGSFE-LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSV 59 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 F++G + P KR I++V+Q L+PHM +++N+A+ +R + K++I+ V A + Sbjct: 60 FLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGV 119 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L + L R P LSGG++QR ++ R++ PK+ L DEP S LDA R R E+ K + Sbjct: 120 LGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLR-EMLKKA 178 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 TT+++VTHD + LA+R+VV+ G + QVG P ++ RP+ FVA F+G+ Sbjct: 179 IADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT--- 235 Query: 241 NVIPATITA-TGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDL 288 NV+ T+ A G+ T + G + + D +E G+ + +RPE++ Sbjct: 236 NVLKGTVKALEGKLTVIDAEGMEIYSAD----PAEPGENVTVSIRPEEI 280 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: 246 Number of extensions: 11 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: 353 Length adjustment: 29 Effective length of query: 333 Effective length of database: 324 Effective search space: 107892 Effective search space used: 107892 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