Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate Ga0059261_2227 Ga0059261_2227 aminodeoxychorismate synthase, component I, bacterial clade
Query= curated2:Q9HS66 (488 letters) >FitnessBrowser__Korea:Ga0059261_2227 Length = 587 Score = 213 bits (543), Expect = 1e-59 Identities = 121/260 (46%), Positives = 159/260 (61%), Gaps = 2/260 (0%) Query: 210 RAAFESRVRRIQDAIRDGDTFQANVSHRLDAPAAVHPVAVFEALRDTNPAPYSGIVEFPG 269 RAA+++ R+ D I GD +QAN+S R P+A + A+R A Y GIV Sbjct: 118 RAAYDAAFARVHDWIEAGDIYQANLSFRASVRMLGDPLAAYAAIRARAAAGYGGIVWTGD 177 Query: 270 VDLVSASPELLLARRGRELTTEPIAGTRPRGATPAEDDAARAALRADDKERAEHAMLVDL 329 L+S SPEL A R EL P+ GT PRGATP ED+AARA L D K+RAE+ M+VDL Sbjct: 178 DWLLSFSPELFFALRDGELIARPMKGTTPRGATPEEDEAARATLATDAKQRAENLMIVDL 237 Query: 330 ERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVTGRLRDSCSLRDAIAAVFPGGTITG 389 RNDL +++ GSV VP+ +V+ Y + +VS V+ RL D + D +AA FP G+ITG Sbjct: 238 MRNDLTRIAAPGSVRVPELFKVETYPTLHTMVSTVSARLADGTGIADVLAATFPCGSITG 297 Query: 390 APKPRTMALIDTVEATRRGPYTGSLAAIGFDGDATLSITIRT--LVRRAATYHLRVGAGI 447 APK R M +ID VE RGPYTGS+ I +GDA ++ IRT L R + T + +G+G+ Sbjct: 298 APKIRAMEVIDAVEPDARGPYTGSIGRIDPNGDAAFNVAIRTLHLPRVSETASIGLGSGV 357 Query: 448 VHDSTPAAEYDETLAKARAL 467 V DS E+DE LAK L Sbjct: 358 VADSRAGEEWDECLAKGAFL 377 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: 813 Number of extensions: 41 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: 488 Length of database: 587 Length adjustment: 35 Effective length of query: 453 Effective length of database: 552 Effective search space: 250056 Effective search space used: 250056 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