Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 137 bits (344), Expect = 7e-37 Identities = 79/196 (40%), Positives = 115/196 (58%), Gaps = 6/196 (3%) Query: 17 TVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEPKDRG 76 TVL+ ++ ++ GE + LLG SG GKSTLL +AGL+ + G++ + +T +G Sbjct: 29 TVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGHLMTGPA---KG 85 Query: 77 IGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPSELSG 136 I MVFQS+AL+P +TVE+N+ GL+ A + AE E+R A +++ + P ELSG Sbjct: 86 ISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYESAYPKELSG 145 Query: 137 GQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLK---NTMIYVTHD 193 G RQRV RALV DV L DEP S LD LR ++ L K ++ V+H+ Sbjct: 146 GMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPTKGILLVSHN 205 Query: 194 QIEALTLADRIAVMKS 209 EA+++ADR+ V S Sbjct: 206 IEEAVSMADRVLVFSS 221 Lambda K H 0.320 0.137 0.392 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: 359 Number of extensions: 22 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: 361 Length of database: 452 Length adjustment: 31 Effective length of query: 330 Effective length of database: 421 Effective search space: 138930 Effective search space used: 138930 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