Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_011841694.1 RSPH17029_RS12485 aminodeoxychorismate synthase component I
Query= BRENDA::P20580 (492 letters) >NCBI__GCF_000015985.1:WP_011841694.1 Length = 381 Score = 191 bits (485), Expect = 4e-53 Identities = 115/274 (41%), Positives = 160/274 (58%), Gaps = 3/274 (1%) Query: 208 EAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQVVPSQRMSIEFKA-APIDLYRAL 266 EA + R FR R DY+ A GR+ YI AGDC QV + + +A + + LY AL Sbjct: 97 EAGEVRLAPFRPRIARADYDAAFGRLMAYIAAGDCYQVNLTFPLDGRLEAGSALGLYGAL 156 Query: 267 RCFNPTPYMYFFNFGDFHVVGSSPEVLVRVE-DGLVTVRPIAGTRPRGINEEADLALEQD 325 R P F + G + +SPE+ + +G ++ RP+ GT PR + D L + Sbjct: 157 RARQPVGQGAFCDLGGPVAISASPELFFDCDAEGRISTRPMKGTAPRDPDPARDAELAKI 216 Query: 326 LLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGL 385 L S K AE+LM++DL RND+GR++++G+V+V E IE Y+ V +VS VTG+L Sbjct: 217 LGSSEKGRAENLMIVDLLRNDIGRIAELGSVRVPELFAIESYATVHQMVSRVTGRLIGWP 276 Query: 386 SAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRT- 444 L A+ P G+++GAPKIRAMEII ELEP RG+Y GA+G++A +G +AIRT Sbjct: 277 GLSGLLPALFPCGSVTGAPKIRAMEIIGELEPFPRGLYCGAMGWMAPDGRAAFNVAIRTL 336 Query: 445 AVIKNGELHVQAGGGIVADSVPALEWEETINKRR 478 + GEL + GGGIV DS EWEE + K R Sbjct: 337 RLFPGGELRLDVGGGIVQDSTAPGEWEEALWKTR 370 Lambda K H 0.321 0.139 0.408 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: 521 Number of extensions: 26 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: 492 Length of database: 381 Length adjustment: 32 Effective length of query: 460 Effective length of database: 349 Effective search space: 160540 Effective search space used: 160540 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: 51 (24.3 bits)
This GapMind analysis is from Apr 16 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