Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_017549241.1 C792_RS0109535 aminodeoxychorismate/anthranilate synthase component II
Query= curated2:Q8KGA2 (366 letters) >NCBI__GCF_000330705.1:WP_017549241.1 Length = 192 Score = 70.5 bits (171), Expect = 3e-17 Identities = 59/175 (33%), Positives = 84/175 (48%), Gaps = 19/175 (10%) Query: 178 HVVAFDYGIKTNIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYA 236 H +F Y NI++ L G +TV N +E+ A+ PD I LS GP P Sbjct: 7 HYDSFTY----NIVQFLGECGEDITVRRNDAVQLNEIEALQPDLILLSPGPRTPEQTGMT 62 Query: 237 IDTIRELAARNSTLPIFGICLGHQLLSLAFG---AKTYKLKFG-----HHGANHPVKNLL 288 ++ I + LPIFG+CLGHQ ++ AFG KT +L G HH + + Sbjct: 63 LEVIDKF---KGILPIFGVCLGHQSIAHAFGGNIVKTGRLMHGKTSQIHHDGIGIFRGIP 119 Query: 289 SNTIEITSQNHGFAVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEA 343 T E+ + H V+ SLP E++ +N V IRHR+ VQ+HPE+ Sbjct: 120 QGT-EVMNY-HSLVVDRASLPDCFEVSAEN-EKGEVMAIRHRDFSIEGVQFHPES 171 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: 195 Number of extensions: 10 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: 192 Length adjustment: 25 Effective length of query: 341 Effective length of database: 167 Effective search space: 56947 Effective search space used: 56947 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 Jul 26 2024. The underlying query database was built on Jul 25 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