Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_051301905.1 A3GO_RS22795 aminodeoxychorismate synthase, component I
Query= curated2:P14953 (494 letters) >NCBI__GCF_000428045.1:WP_051301905.1 Length = 479 Score = 282 bits (722), Expect = 2e-80 Identities = 166/471 (35%), Positives = 261/471 (55%), Gaps = 19/471 (4%) Query: 20 PVTMEVYADMETPISLFKRFEESSCCFLLESVEGGEKWARYSIIGKNPFLVVESYKNKTI 79 P + +E LF L+S + G K ARY ++ +P + + +T Sbjct: 6 PTLLRELPYIEDTSRLFAPLAGQPWAMFLDSSDRGSKQARYDLVTCDPMATLVTRNGRTR 65 Query: 80 IRERNGSQREVEGNPVEIIKGIMGKFKGANLPNLPRFNGGAVGYFGYDLIRHYENLPNVP 139 I +GS E P+ +++ ++ + + + +LP F GGA+GYF YDL R E LP V Sbjct: 66 ITRADGSVVVSEDEPMGLLQALLRQHRMDSHESLP-FRGGALGYFSYDLARSLERLPVVA 124 Query: 140 EDDMGLPECHFMFTDEVLVYDHLKQKIHIIVNLHVNGNIERAYISAVDRI--KTIHREIL 197 D LPE D LV DH +Q+ +V + + V+R + E + Sbjct: 125 RDQDQLPEMAIGIYDWALVVDHQEQR-SWLVGCGFDSRTVTQWPMLVERFCRPPVMVEPV 183 Query: 198 DTRWKTADNSVLSYNKKKNELAVTSNISKEDFCRNVLKAKQYIRDGDIFQVVLSQRLCVE 257 R K AV N+S++ + + K+YI++GD +QV L+QR V Sbjct: 184 PFRVKG---------------AVEFNMSRQQYADAFREIKRYIQEGDCYQVNLAQRFSVA 228 Query: 258 TNENPFNIYRALRVINPSPYMYYLKFGGYRIIGSSPEMLVRVENGIVETCPIAGTRKRGR 317 T +P+ Y+ LR +NP+P+ YL +++ SSPE + + +G+ ET PI GT RG Sbjct: 229 TEGDPWQAYQQLRRLNPAPFSAYLNTPAAQLLCSSPERFLAIRDGLAETRPIKGTLPRGT 288 Query: 318 TKEEDEALEKELLSDEKEIAEHVMLVDLGRNDIGRVSKFGTVAVKNLMHIERYSHVMHVV 377 T ++D AL++ LL+ EK+ AE++M+VDL RND+G+ S GTV V L +E Y+ V H+V Sbjct: 289 TTQDDRALKQRLLASEKDRAENLMIVDLLRNDLGKNSALGTVEVGELFGLESYATVHHLV 348 Query: 378 TNVQGEIREDKTPFDALMSILPAGTLSGAPKVRAMEIIDELETVKRGPYGGAIGYLSFNG 437 + + + ++ D L P G+++G PK+RAMEII++LE +RG Y G+IGY+ F+G Sbjct: 349 STISSRLAANRDALDLLRGCFPGGSITGTPKLRAMEIIEQLEPDRRGVYCGSIGYIGFDG 408 Query: 438 NLDSCITIRTIILKDGKAYVQAGAGIVADSVPEREYEECYNKAMALLKAIE 488 N+DS I IRT++ DG+ AG G+VADSV + EY+E ++KA A+L+ ++ Sbjct: 409 NMDSNIAIRTMVHIDGRMRFWAGGGLVADSVLDSEYQETFHKANAMLRLLQ 459 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: 530 Number of extensions: 22 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: 1 Length of query: 494 Length of database: 479 Length adjustment: 34 Effective length of query: 460 Effective length of database: 445 Effective search space: 204700 Effective search space used: 204700 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: 52 (24.6 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