Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_009566395.1 RSPH17029_RS03635 aminodeoxychorismate/anthranilate synthase component II
Query= curated2:Q8KGA2 (366 letters) >NCBI__GCF_000015985.1:WP_009566395.1 Length = 195 Score = 90.1 bits (222), Expect = 4e-23 Identities = 60/178 (33%), Positives = 90/178 (50%), Gaps = 11/178 (6%) Query: 189 NIIRQLNAEGCKVTVV-NAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTIRELAARN 247 N++ L G +V V N + M+PD I LS GP DP A + AA Sbjct: 14 NLVHYLGELGAEVVVRRNDALDVQAAMGMHPDAIVLSPGPCDPAAAGICLPLTA--AAAE 71 Query: 248 STLPIFGICLGHQLLSLAFGAKT---YKLKFGHHGA-NHPVKNLLSNTIE--ITSQNHGF 301 + +P+ G+CLGHQ + AFG K +++ G GA +H K + + + ++ H Sbjct: 72 ARIPLLGVCLGHQTIGQAFGGKVVRCHEIVHGKMGAMHHEGKGVFAGLPSPFLATRYHSL 131 Query: 302 AVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEAAPGPHDSHYLFKEFTE 359 VE +SLP LE+T L D T+ G+RH+ LP VQ+HPE+ H H + + F + Sbjct: 132 VVERDSLPDCLEVT-AWLEDGTIMGLRHKSLPIEGVQFHPESIASEH-GHQMLRTFLD 187 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: 191 Number of extensions: 12 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: 366 Length of database: 195 Length adjustment: 25 Effective length of query: 341 Effective length of database: 170 Effective search space: 57970 Effective search space used: 57970 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 16 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