Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 143 bits (360), Expect = 1e-38 Identities = 87/217 (40%), Positives = 129/217 (59%), Gaps = 11/217 (5%) Query: 2 TGLL-LKDIRKSYGAVD-----VIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEI 55 T LL L+ +RK++ D V+ G+D ++EGE V +G SG GKSTLLR++AGL + Sbjct: 8 TALLDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKA 67 Query: 56 TGGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVR 115 GG++ G + P+K GI+MVFQS+AL+P +TV +N+ G+ A +K E + R Sbjct: 68 NGGEVKYRGHLMTG--PAK-GISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERAN 124 Query: 116 GAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIE 175 A D++ L Y PK LSGG RQRV RA+ P V L DEP S LD R + Sbjct: 125 EAIDLIGLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLRED 184 Query: 176 IAKLSERMSDTT--MIYVTHDQVEAMTLADRIVVLSA 210 + +L + T ++ V+H+ EA+++ADR++V S+ Sbjct: 185 LLELWDERKIPTKGILLVSHNIEEAVSMADRVLVFSS 221 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: 387 Number of extensions: 20 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: 452 Length adjustment: 31 Effective length of query: 331 Effective length of database: 421 Effective search space: 139351 Effective search space used: 139351 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 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