Align Carbamoyl-phosphate synthase arginine-specific small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate WP_012589547.1 MSIL_RS02570 type 1 glutamine amidotransferase
Query= curated2:P54324 (354 letters) >NCBI__GCF_000021745.1:WP_012589547.1 Length = 201 Score = 65.1 bits (157), Expect = 1e-15 Identities = 55/178 (30%), Positives = 82/178 (46%), Gaps = 17/178 (9%) Query: 176 SILQSLLARGCRVTVVPHDT-APEAIDALKPDGLVLSNGPGDPKQLRHQLPAIRQLIDRY 234 +++ L + G VTV +D + E I A PDG+VLS GP P + L I+ Sbjct: 16 NLVHCLGSLGADVTVHRNDKISVEEIMAAAPDGIVLSPGPCGPPEAGICLELIKAAAPTI 75 Query: 235 PTLAICLGHQLVALATGR--IR-------KKLRFGHRGANQPVWDAVKQNVMMTSQNHSY 285 P +CLGHQ + A G +R K H+G + ++ + + HS Sbjct: 76 PIFGVCLGHQALGEAYGGEIVRAPAPVHGKIATIDHQG--EALFHGI-NGPFRAVRYHSL 132 Query: 286 VVKEGSLVGKPFDIRFINVNDGSVEGIVHRHKPILSVQYHPEAHPGPHDTGYIFDEFL 343 VV+ + P D++ DG + G+ HRH P VQ+HPE+ H IF+ FL Sbjct: 133 VVRAET---APADLKVTAQTDGLIMGLSHRHFPAHGVQFHPESIASEHGM-RIFENFL 186 Lambda K H 0.320 0.138 0.410 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: 198 Number of extensions: 8 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: 354 Length of database: 201 Length adjustment: 25 Effective length of query: 329 Effective length of database: 176 Effective search space: 57904 Effective search space used: 57904 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 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