Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_011937544.1 GURA_RS03090 aminodeoxychorismate synthase component I
Query= curated2:Q9Z4W7 (511 letters) >NCBI__GCF_000016745.1:WP_011937544.1 Length = 574 Score = 184 bits (468), Expect = 6e-51 Identities = 109/280 (38%), Positives = 154/280 (55%), Gaps = 4/280 (1%) Query: 222 PLAAATPAD-HGTQGWTANLTEAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTD 280 P A PA+ + T GWT +L A+ VA RE IA G +Q+ + R P Sbjct: 84 PSAEVPPAEAYQTSGWTTSLDGAEHARAVASIRELIACGHTYQVNFTMRQHFRFTGDPAA 143 Query: 281 LYRHLRATNPSPYMYHLSLGGGRHVIGASPELLVKAEGRTVRTRPLAGTRPRHPDPAEDL 340 Y LR P+PY ++ G + ++ ASPEL + TRP+ GT R ED Sbjct: 144 FYSDLRRCQPTPYSAYIDTGRFQ-ILSASPELFFSLREGVLTTRPMKGTAGRGRWWQEDE 202 Query: 341 RLERELRADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLSSTVRGR 400 +++LR KERAE++M+VDL RND+G V+ G+VRV L VE V ++ST++ R Sbjct: 203 EAKQKLRESPKERAENLMIVDLLRNDMGMVSTTGSVRVNSLFDVETLGTVHQMTSTIQSR 262 Query: 401 LAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFVGADGLTDFAI 460 L +G ++ FP G+++GAPK R MEIIAELE RGVY G +G+V F++ Sbjct: 263 LKDGVGLTGLFQALFPCGSVTGAPKKRTMEIIAELEDSPRGVYTGCIGYVSPGDEAQFSV 322 Query: 461 ALRTMVV--ADGHVHVQAGAGIVADSDPAAEFRETLHKSR 498 A+RT+V+ A G + G+G+ DS AE+ E L K R Sbjct: 323 AIRTIVIDAATGRGELGIGSGVTFDSQADAEYAECLAKGR 362 Lambda K H 0.319 0.134 0.394 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: 606 Number of extensions: 28 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: 511 Length of database: 574 Length adjustment: 35 Effective length of query: 476 Effective length of database: 539 Effective search space: 256564 Effective search space used: 256564 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: 52 (24.6 bits)
This GapMind analysis is from Apr 12 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