Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate Dsui_0001 Dsui_0001 aminodeoxychorismate synthase, component I
Query= curated2:Q9HS66 (488 letters) >FitnessBrowser__PS:Dsui_0001 Length = 606 Score = 197 bits (501), Expect = 9e-55 Identities = 118/259 (45%), Positives = 157/259 (60%), Gaps = 2/259 (0%) Query: 210 RAAFESRVRRIQDAIRDGDTFQANVSHRLDAPAAVHPVAVFEALRDTNPAPYSGIVEFPG 269 +AA + V+RI+D I GD +Q N + L A HP+A++ LR P P G+V Sbjct: 136 QAAHAAAVQRIRDYIAAGDCYQVNFTFPLHFQAYGHPLALYARLRQRQPTPLGGLVLTAE 195 Query: 270 VDLVSASPELLLARRGRELTTEPIAGTRPRGATPAEDDAARAALRADDKERAEHAMLVDL 329 ++S SPEL +ARRG L T P+ GT PRGA A D A RAAL A K+RAE+ M+VDL Sbjct: 196 RRILSLSPELFVARRGDTLRTRPMKGTAPRGADEAGDAANRAALAASAKDRAENLMIVDL 255 Query: 330 ERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTITG 389 RNDLG++++ GSV V + ++ Y V + S V+ R + +AA+FP G+ITG Sbjct: 256 LRNDLGRLAQTGSVRVEELFAIETYPSVFQMTSTVSAR-APGVGPGETLAALFPCGSITG 314 Query: 390 APKPRTMALIDTVEATRRGPYTGSLAAIGFDGDATLSITIRTLVRRA-ATYHLRVGAGIV 448 APK R M +I+ +E RG YTGSL + DGD L++ IR+L A + VG+GIV Sbjct: 315 APKLRAMEIIEELEVGPRGLYTGSLGLLAPDGDFCLNVAIRSLELGADGRGVMGVGSGIV 374 Query: 449 HDSTPAAEYDETLAKARAL 467 DS PAAEY E L KAR L Sbjct: 375 TDSEPAAEYRECLLKARFL 393 Lambda K H 0.317 0.135 0.397 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: 770 Number of extensions: 46 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: 488 Length of database: 606 Length adjustment: 35 Effective length of query: 453 Effective length of database: 571 Effective search space: 258663 Effective search space used: 258663 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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