Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 156 bits (394), Expect = 4e-43 Identities = 89/220 (40%), Positives = 132/220 (60%), Gaps = 7/220 (3%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 MIS +V K Y VL D S +++G + + G SG+GK+TL+K +N L G + + Sbjct: 1 MISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAI 60 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQL 120 +G +A + +LR R+G VFQ LFPH+S+ +N+ + ++ G +EE + + +L Sbjct: 61 EGRDVAAQP--VAELRRRIGYVFQGIGLFPHMSVAENVALVP-RLQGVPREERAARVAEL 117 Query: 121 LERVGLSAH-AKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVM 179 L+ V L A A++ P QLSGGQ QRV ARALA P +ML DEP ALDP + + L Sbjct: 118 LDLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDP-VTRDELGAA 176 Query: 180 VQLAHE--GMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217 + HE G+T + VTH+M A +ADRVI + +G+I+ D Sbjct: 177 YRALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILAD 216 Lambda K H 0.321 0.135 0.390 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: 133 Number of extensions: 5 Number of successful extensions: 4 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: 244 Length of database: 252 Length adjustment: 24 Effective length of query: 220 Effective length of database: 228 Effective search space: 50160 Effective search space used: 50160 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 (21.9 bits) S2: 46 (22.3 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