Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_029132998.1 A3GO_RS0108270 aminodeoxychorismate synthase, component I
Query= curated2:P14953 (494 letters) >NCBI__GCF_000428045.1:WP_029132998.1 Length = 461 Score = 271 bits (694), Expect = 3e-77 Identities = 168/459 (36%), Positives = 247/459 (53%), Gaps = 21/459 (4%) Query: 34 SLFKRFEESSCCFLLESVEGGEKWARYSIIGKNPFLVVESYKNKTIIRERNGSQREVEGN 93 +LF R E S L+S RY I+ +P+L + + N T IR S R + Sbjct: 15 ALFARIAEKSWAVFLDSGYPRTSAGRYDILAADPYLTLTTRANITEIRGE-ASIRLSPDD 73 Query: 94 PVEIIKGIMGKF--KGANLPNLPRFNGGAVGYFGYDLIRHYENLPNVPEDDMGLPECHFM 151 P +++ ++G A+LP F GGA+G+F YDL E LP P++ +PE Sbjct: 74 PFALLQEVLGAHTESAADLP----FGGGAIGWFSYDLAWRIERLPEQPDNRDQVPEMVIG 129 Query: 152 FTDEVLVYDHLKQKIHIIVNLHVNGNIERAYISAVDRIKTIHREILDTRWKTADNSVLSY 211 D +V DH + ++ ER + S + T R + + Sbjct: 130 LYDWAVVVDHKLCRSWLVAEGRDQRTRERWW-SLIKLFCTPSRPRIKRPFHITG------ 182 Query: 212 NKKKNELAVTSNISKEDFCRNVLKAKQYIRDGDIFQVVLSQRLCVETNENPFNIYRALRV 271 + SN+ + + + KQYI DGD +QV +QR + ++ Y+ LR Sbjct: 183 -------PIRSNMDRATYVAAFQRIKQYILDGDCYQVNFAQRFSAPAEGDGWSAYQELRR 235 Query: 272 INPSPYMYYLKFGGYRIIGSSPEMLVRVENGIVETCPIAGTRKRGRTKEEDEALEKELLS 331 +NP+P+ YLK I+GSSPE ++++ VET PI GTR RG T E D A+ +EL S Sbjct: 236 MNPAPFSAYLKTPHAEILGSSPERFLKLKGKQVETKPIKGTRPRGDTPEGDSAMARELAS 295 Query: 332 DEKEIAEHVMLVDLGRNDIGRVSKFGTVAVKNLMHIERYSHVMHVVTNVQGEIREDKTPF 391 K+ AE++M+VDL RND+GRV GTV V + +E Y+ V H+V+ V GE+RED+ Sbjct: 296 SSKDRAENLMIVDLLRNDLGRVCNAGTVKVPEIFSVESYATVHHLVSTVTGELREDQDAI 355 Query: 392 DALMSILPAGTLSGAPKVRAMEIIDELETVKRGPYGGAIGYLSFNGNLDSCITIRTIILK 451 L + P G+++GAPK+RAMEII ELE RGPY G+I Y+ F+G +DS I IRT++ Sbjct: 356 GLLRACFPGGSITGAPKIRAMEIIAELEPDCRGPYCGSIAYIGFDGRMDSNIVIRTLVYN 415 Query: 452 DGKAYVQAGAGIVADSVPEREYEECYNKAMALLKAIEEA 490 G+ AG GIV DS EY+E ++KA ALL+ ++E+ Sbjct: 416 QGEICCWAGGGIVHDSEVNAEYQETFDKASALLRLLKES 454 Lambda K H 0.319 0.138 0.401 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: 536 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 494 Length of database: 461 Length adjustment: 34 Effective length of query: 460 Effective length of database: 427 Effective search space: 196420 Effective search space used: 196420 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 (21.7 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