Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_011779879.1 MVAN_RS13375 carbamoyl-phosphate synthase small subunit
Query= curated2:Q9YGB2 (192 letters) >NCBI__GCF_000015305.1:WP_011779879.1 Length = 376 Score = 64.3 bits (155), Expect = 3e-15 Identities = 47/153 (30%), Positives = 71/153 (46%), Gaps = 13/153 (8%) Query: 24 RVKVVPNTITVGELRRLDPDGVIISPGPGHPLERREVGNSPEIVLEAGVPILGVCLGHQI 83 R V+P++ T ++ L PDGV +S GPG P + VL AG+P+ G+C G+QI Sbjct: 206 RSVVLPSSATFAQIADLRPDGVFLSNGPGDPATADHIVAVTREVLGAGIPLFGICFGNQI 265 Query: 84 IATAFGGKVGRVKPRH-GKASPVKHDGKGVLRGIKNPLTAGRYHSLAVLEVPREFD---- 138 + A G ++ H G PV G + +TA + E + FD Sbjct: 266 LGRALGLSTYKMVFGHRGINIPVIDHATG-----RVAITAQNHGFALEGEAGQTFDTPFG 320 Query: 139 ---VSAVSLDDNVVMGIRHRKLPIEGLQFHPES 168 VS +D VV G+R + +Q+HPE+ Sbjct: 321 DAEVSHTCANDGVVEGVRLKSGRAFSVQYHPEA 353 Lambda K H 0.320 0.141 0.422 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: 221 Number of extensions: 12 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: 192 Length of database: 376 Length adjustment: 25 Effective length of query: 167 Effective length of database: 351 Effective search space: 58617 Effective search space used: 58617 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