Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_086511656.1 BZY95_RS20045 aminodeoxychorismate synthase, component I
Query= curated2:P05378 (462 letters) >NCBI__GCF_002151265.1:WP_086511656.1 Length = 459 Score = 247 bits (631), Expect = 5e-70 Identities = 170/444 (38%), Positives = 239/444 (53%), Gaps = 19/444 (4%) Query: 21 AYLKLAEKAPVSFLLESVERGRQS-RFSIVGVGARRTFRLKD-GVFTVNGERVETRDPLR 78 AY + + P + LL+S + R+ I+ F + GV ++GE + RDP Sbjct: 18 AYFQALRQRPGAVLLDSGKPAAPGGRYDIISSDPVSAFTVDGKGVIRIDGEVQQGRDPFM 77 Query: 79 ALYERVYAPLERHPDLP-PFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVV 137 A + P PF GG++GY YDL R E + + + + LP + Sbjct: 78 AQQTLLEGLALDVPSSDLPFLGGLIGYWGYDLGRSLEPVGNSAQERVCLPACRTGLYDWA 137 Query: 138 AVFDHLKNLLHLVAPGRDPEEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSREAY 197 + DH + LVA AE RL E P +P G A F+ + R+ Y Sbjct: 138 LIQDHQRQESWLVAT------AERRLQVMEWLRHSAAPTLP---FGLLAPFEGEMDRDGY 188 Query: 198 LEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPSPYMGYL----DLGE 253 DYIRAGD +Q+ L+ R S+P + + Y LR P+P+ G++ + GE Sbjct: 189 ARRFAAVQDYIRAGDCYQINLAQRFSAPYSGDLWDAYLRLRLATPTPFAGFMAWPSERGE 248 Query: 254 VVLVSASPESLL--RSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLL 311 ++S SPE L SDG V TRPI GTRPRG EED +LA EL+ K+ AE+VM++ Sbjct: 249 QAILSLSPERFLLCESDGH-VETRPIKGTRPRGSTPEEDWQLAMELISSLKDRAENVMIV 307 Query: 312 DLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTV 371 DL RND+GRV G+VRV + +E Y++V HLVS V G LA K PLD LA+ P G++ Sbjct: 308 DLLRNDLGRVCQPGSVRVPQLCGLESYANVHHLVSVVCGRLAAEKRPLDLLAAAFPGGSI 367 Query: 372 SGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGI 431 +GAPK+RAM+II+ELEP RR Y GS G++ G MD ++ +RT V +H+ G G+ Sbjct: 368 TGAPKVRAMQIIDELEPSRRSVYCGSLGFVDVRGNMDTSIAIRTAVADGERIHLWGGGGL 427 Query: 432 VADSVPEREYEECWNKARALLKAV 455 VADS E EY E +K R L++A+ Sbjct: 428 VADSSVEAEYVETLDKIRHLMQAL 451 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: 565 Number of extensions: 21 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: 462 Length of database: 459 Length adjustment: 33 Effective length of query: 429 Effective length of database: 426 Effective search space: 182754 Effective search space used: 182754 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 10 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