Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_011385238.1 AMB_RS14405 type 1 glutamine amidotransferase
Query= curated2:Q8KGA2 (366 letters) >NCBI__GCF_000009985.1:WP_011385238.1 Length = 196 Score = 88.2 bits (217), Expect = 2e-22 Identities = 57/178 (32%), Positives = 85/178 (47%), Gaps = 12/178 (6%) Query: 189 NIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTIRELAARN 247 N+ L G +V V N T D+VL + P GI +S GP DP ++ I A Sbjct: 14 NLWHYLGELGAEVVVKRNDAVTVDQVLGLRPQGIVISPGPCDPDRAGICLELIERAAG-- 71 Query: 248 STLPIFGICLGHQLLSLAFGAKTYKLKFGHHGANHPVKNLLSNTIE------ITSQNHGF 301 T+P+FG+CLGHQ + AFG K + HG + + + + ++ H Sbjct: 72 -TIPLFGVCLGHQAIGQAFGGKVVRAPKPMHGKVDTITHDDTGVFQGLPSPFRATRYHSL 130 Query: 302 AVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEAAPGPHDSHYLFKEFTE 359 VE ES P L ++ D V G+ H+ELP + VQ+HPE+ H H + + F + Sbjct: 131 VVERESFPDCLHVSAWTA-DGLVMGLAHKELPIWGVQFHPESIETEH-GHAMLRNFID 186 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: 203 Number of extensions: 9 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: 366 Length of database: 196 Length adjustment: 25 Effective length of query: 341 Effective length of database: 171 Effective search space: 58311 Effective search space used: 58311 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 Aug 03 2021. The underlying query database was built on Aug 03 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