Align Anthranilate synthase component 1 1; EC 4.1.3.27; Anthranilate synthase component I 1 (uncharacterized)
to candidate WP_245526306.1 NITSA_RS01450 aminodeoxychorismate synthase component I
Query= curated2:Q5V448 (489 letters) >NCBI__GCF_000186245.1:WP_245526306.1 Length = 343 Score = 114 bits (284), Expect = 7e-30 Identities = 88/285 (30%), Positives = 141/285 (49%), Gaps = 27/285 (9%) Query: 190 GDPSVEDPPVETDEATFESDCTRESFADRVQTVKQYIRDGDTFQANVSQRLRAPAAVHPV 249 G+P D P ++ + S+A ++ +K+ IR G+T+ N L P+ + Sbjct: 72 GEPPDTDTPFSGEKDLYIEPIPYRSYAQALERIKEEIRRGNTYLLN----LTFPSLIETT 127 Query: 250 EAFDALRTVNPAPYSALLEFPGVDLVSASPELLLHRDGDRIETEPIAGTRPRGETPDADD 309 + + + APY LL V SPE + +RI T P+ GT + A+ Sbjct: 128 LSLEEIYRAADAPYKLLLP---EQFVCFSPEKFITIQKNRIYTYPMKGTIDATLSNAAEK 184 Query: 310 RLETDLLDDEKERAEHAMLVDLERNDLGKVSKFGSVEVSDYRRVDRY----SEVMHLVSV 365 +L D KE AEH M+ DL RNDL ++S+ V V +R +D+ E+ + S Sbjct: 185 -----ILADPKEMAEHVMITDLMRNDLNRISE--KVRVEKFRYLDKIHAGEKELYQVSSE 237 Query: 366 VEGRLRDGASLQDAIAAVF----PGGTITGAPKPRTMEIIDEVEATRRGPYTGSIGLF-G 420 + G L G + + I ++ P G+I+G PK +T++II EVE RG YTG G+ G Sbjct: 238 IVGEL--GGNWRSRIGSILREITPAGSISGTPKKKTLQIIKEVEGYDRGFYTGIFGVCKG 295 Query: 421 FDGRATLNIVIRTLVRYAEEYHLRVGAGVVHDSDPDREYQETLDK 465 + R+ ++IR + + + + G G+ DSDP EY+E L+K Sbjct: 296 EELRSA--VLIRFVEKSGKGLVYKSGGGITIDSDPLSEYRELLEK 338 Lambda K H 0.317 0.135 0.396 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: 370 Number of extensions: 18 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: 489 Length of database: 343 Length adjustment: 31 Effective length of query: 458 Effective length of database: 312 Effective search space: 142896 Effective search space used: 142896 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 (21.6 bits) S2: 50 (23.9 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