Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate HSERO_RS07665 HSERO_RS07665 anthranilate synthase
Query= curated2:Q9Z4W7 (511 letters) >FitnessBrowser__HerbieS:HSERO_RS07665 Length = 615 Score = 187 bits (476), Expect = 7e-52 Identities = 124/304 (40%), Positives = 172/304 (56%), Gaps = 26/304 (8%) Query: 226 ATPADHGTQGWTANLT----EAQFTERVARAREHIAAGDAFQIVLSRRLSRPLRARPTDL 281 A AD T G ANL EA F+ +AR R++IAAGD +Q+ + RL + L Sbjct: 106 ADGADMFTSGGIANLRSSVDEAAFSAAIARIRDYIAAGDTYQVNYTYRLHGDVHGDAIGL 165 Query: 282 YRHLRATNPSPY--MYHLSLGGGRHVIGASPELLVKAEGRTVRTRPLAGTR---PRHPDP 336 YR LRA P PY + LGG V+ SPEL V + ++ +P+ GT P + Sbjct: 166 YRRLRARQPVPYGALVRDELGG--MVLSCSPELFVSHQQGVLKAKPMKGTARALPPEQEG 223 Query: 337 AEDLRLERELR--ADEKERAEHVMLVDLGRNDLGRVTEPGTVRVERLMRVERFSHVMHLS 394 AE + +R L ADEK RAE++M+VDL RNDLGRV PG+V+V L V R+ V+ ++ Sbjct: 224 AETVNAQRALALAADEKNRAENLMIVDLLRNDLGRVAVPGSVQVPHLFDVRRYGQVLQMT 283 Query: 395 STVRGRLAEGRDALDALRSAFPAGTLSGAPKIRAMEIIAELEPEQRGVYGGALGFV---- 450 ST+R RL E D + + +P G+++GAPK R MEII ELE E RG+Y GA+G+ Sbjct: 284 STIRARLREHATLADTINALYPCGSITGAPKRRTMEIIHELESEPRGLYTGAIGWFDAPR 343 Query: 451 -GADGLTDF--AIALRTMVVADGHVHVQ-----AGAGIVADSDPAAEFRETLHKSRAMLT 502 G + DF ++ +RT+ + H ++ GAGIV DS AAEF E KS + LT Sbjct: 344 PGGPAIGDFCLSVPIRTLELQAPHAGLRKAVMGVGAGIVHDSQAAAEFAECQLKS-SFLT 402 Query: 503 AVRR 506 + + Sbjct: 403 GLEK 406 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: 754 Number of extensions: 47 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: 511 Length of database: 615 Length adjustment: 36 Effective length of query: 475 Effective length of database: 579 Effective search space: 275025 Effective search space used: 275025 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: 53 (25.0 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