Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_013536998.1 THEAM_RS01225 type 1 glutamine amidotransferase
Query= curated2:Q8KGA2 (366 letters) >NCBI__GCF_000185805.1:WP_013536998.1 Length = 189 Score = 97.1 bits (240), Expect = 3e-25 Identities = 57/162 (35%), Positives = 86/162 (53%), Gaps = 10/162 (6%) Query: 189 NIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTIRELAARN 247 N+++ G V VV N K T E+ ++P + +S GP P +++ IR A + Sbjct: 14 NVVQYFGKLGADVRVVRNDKITVPEIEELHPQALVISPGPCTPREAGVSVEAIRHFAGK- 72 Query: 248 STLPIFGICLGHQLLSLAFGAKTYKLKFGHHGAN----HPVKNLLSNTIEITS--QNHGF 301 LPIFGICLGHQ + AFGAK + K HG H + L + S + H Sbjct: 73 --LPIFGICLGHQSIGFAFGAKIVRAKKLMHGKASNIVHDGRYLFNGMKNPFSAIRYHSL 130 Query: 302 AVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEA 343 ++ E+LP + E+T ++ D + GIRHR+ P + VQ+HPE+ Sbjct: 131 VIDRETLPSDFEITAESEDDREIMGIRHRKYPIYGVQFHPES 172 Lambda K H 0.317 0.134 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: 207 Number of extensions: 12 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: 366 Length of database: 189 Length adjustment: 25 Effective length of query: 341 Effective length of database: 164 Effective search space: 55924 Effective search space used: 55924 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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