Align Aminodeoxychorismate/anthranilate synthase component 2; ADC synthase; ADCS; 4-amino-4-deoxychorismate synthase component 2; Aminodeoxychorismate synthase, glutamine amidotransferase component; EC 2.6.1.85; EC 4.1.3.27 (characterized)
to candidate WP_078430671.1 BK574_RS26020 carbamoyl phosphate synthase small subunit
Query= SwissProt::P28819 (194 letters) >NCBI__GCF_002019605.1:WP_078430671.1 Length = 362 Score = 67.0 bits (162), Expect = 4e-16 Identities = 44/148 (29%), Positives = 73/148 (49%), Gaps = 10/148 (6%) Query: 26 LVVKRNDSITIDEIEELSPDFLMISPGPCSPDEAGISLEAIKHFAGKIPIFGVCLGHQSI 85 +VV N S +EI L PD +M+S GP +P + +E IK GK+PIFG+CLGHQ + Sbjct: 195 IVVPYNTSA--EEILRLYPDGIMLSNGPGNPVDVPEGIEMIKGLLGKVPIFGICLGHQLL 252 Query: 86 AQVFGGDVVRAERLMHGKTSDIEHDGKTIFEGLKNPLVATRYHSLIVKPETLPSCFTVTA 145 A G ++ +L G H + + G + + ++ H ++ ++L + Sbjct: 253 ALACG---AKSAKLTFGHRGS-NHPVRELETGKID--ITSQNHGYTIEKDSLEDTRLIVT 306 Query: 146 Q--TKEGEIMAIRHNDLPIEGVQFHPES 171 + + + H D P VQ+HPE+ Sbjct: 307 HIAVNDETVEGVAHLDYPAFSVQYHPEA 334 Lambda K H 0.320 0.139 0.404 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: 13 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: 194 Length of database: 362 Length adjustment: 25 Effective length of query: 169 Effective length of database: 337 Effective search space: 56953 Effective search space used: 56953 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 09 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