Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate Echvi_0152 Echvi_0152 GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit/GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit
Query= BRENDA::P09786 (200 letters) >FitnessBrowser__Cola:Echvi_0152 Length = 509 Score = 63.5 bits (153), Expect = 6e-15 Identities = 44/143 (30%), Positives = 71/143 (49%), Gaps = 3/143 (2%) Query: 51 LVLSPGPGRPEDAGCMLELLAWARGRLPVLGVCLGHQALALAAGGAVGEARKPLHGKSTS 110 ++LS P D G L RG+LP+LGVC G Q LA GG V + +G++ Sbjct: 47 VILSGSPCSVRDEGSPDVDLEQFRGKLPLLGVCYGSQLLAQKYGGNVTPSEIREYGRANL 106 Query: 111 LRFDQRHPLFDGIA-DLRVARYHSLVVSRLPEGFDCLAD-ADGEIMAMADPRNRQLGLQF 168 D+ + LF ++ +V H + LP+G++ ++ A ++ A P G+QF Sbjct: 107 NFIDKHNDLFHEVSHGSQVWMSHGDTIKELPQGWEVISSTASVKVAAFKVPDEDTFGIQF 166 Query: 169 HPESILTTHGQRLLENALLW-CG 190 HPE + G+ +L N ++ CG Sbjct: 167 HPEVTHSEEGKNVLRNFVVQICG 189 Lambda K H 0.325 0.141 0.436 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: 199 Number of extensions: 11 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: 200 Length of database: 509 Length adjustment: 27 Effective length of query: 173 Effective length of database: 482 Effective search space: 83386 Effective search space used: 83386 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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