Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013134865.1 ARNIT_RS05295 urea ABC transporter ATP-binding protein UrtD
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000092245.1:WP_013134865.1 Length = 262 Score = 124 bits (311), Expect = 2e-33 Identities = 84/260 (32%), Positives = 140/260 (53%), Gaps = 19/260 (7%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L V+ +++ F G A+N++SFS N GE+ IIG NGAGK+T+ + +TG P G + Sbjct: 21 ILLVDGVSVSFDGFKALNNLSFSINYGELRCIIGANGAGKSTMMDVVTGKTRPDEGEVIF 80 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVA-QHNKLIRASGFSI 129 G+ L + IS+ + R FQ +F SV ENL +A + +K + FS Sbjct: 81 ----GEAVNLLELDEPTISE-IGIGRKFQKPTVFQNHSVFENLELAMKDDKRFFKTLFS- 134 Query: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 + E D + + + L E + +AG L +G ++ LEI + EP + Sbjct: 135 ----------KLRSEQKDRIEETMKLIGLKELYNLDAGILSHGQKQWLEIGMLIMQEPKL 184 Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249 L +DEP AG+ P+E + A++LT + E+ V+++EHDM + +I+ V VL G ++ Sbjct: 185 LLVDEPVAGMTPQEVEKTAEILTSLSKEN--AVVVVEHDMEFIRSIASKVTVLHEGSVLA 242 Query: 250 DGDPAFVKNDPAVIRAYLGE 269 +G+ ++N+ V + YLGE Sbjct: 243 EGNMDAIQNNEKVRKVYLGE 262 Lambda K H 0.319 0.137 0.397 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: 172 Number of extensions: 7 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: 294 Length of database: 262 Length adjustment: 25 Effective length of query: 269 Effective length of database: 237 Effective search space: 63753 Effective search space used: 63753 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: 47 (22.7 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