Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_011372097.1 SUDEN_RS02425 aminodeoxychorismate synthase component I
Query= curated2:Q08653 (461 letters) >NCBI__GCF_000012965.1:WP_011372097.1 Length = 312 Score = 116 bits (290), Expect = 1e-30 Identities = 97/280 (34%), Positives = 152/280 (54%), Gaps = 36/280 (12%) Query: 174 FVTEPESNFE--REQFYKVVEKAKKYIVEGDIFQVVLSQAFTFKTTLDPFYIYRALRMIN 231 F+ + +FE +E+F V+EK K +G+ + + L+Q KT L IY A Sbjct: 56 FLQKDGVSFETYKEKFDFVIEKIK----DGETYLLNLTQPTYIKTPLTLQEIYSAAN--- 108 Query: 232 PSPYMFYLKFGDTVVLGSSPETMAKVEGDKATVKPIAGTRPRGRTVEEDLKLEREL-LND 290 +PY L++ D V SPE ++ K + P+ GT ++ + +E+ L D Sbjct: 109 -APYK--LRYKDKFVC-FSPEKFISIKDYKISTFPMKGT------IDASILNAKEIILED 158 Query: 291 EKEIAEHVMLVDLGRNDLGRVCKEGTVRVEKKMVIERYS----HVMHIVSQVSGELKDDK 346 +KE+AEHVM+VDL RNDL V K V+VEK I + ++H+ S +SG++ DD Sbjct: 159 KKEMAEHVMVVDLLRNDLSMVAKN--VKVEKFRYITKIEAGEKKLLHVSSHISGDVGDDW 216 Query: 347 DAV--DVFEATFPAGTVSGAPKVRAMEIIEELEPTPRGPYAGAVGYFSFPDDKGRMNMDS 404 + D+ ++ PAG++SGAPK +EII +E RG ++G G + G + +DS Sbjct: 217 HSKIGDILKSLLPAGSISGAPKKSTLEIIHLVEGYERGYFSGVFGVYD-----GEV-LDS 270 Query: 405 AITIRSFFFKGKQGWL-QAGAGIVYDSVPEREYQETLNKL 443 A+ IR F K K G++ ++G GI DS + EY E L+K+ Sbjct: 271 AVMIR-FVQKTKDGYMYKSGGGITLDSDVKSEYNEMLDKV 309 Lambda K H 0.319 0.137 0.392 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: 376 Number of extensions: 29 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: 461 Length of database: 312 Length adjustment: 30 Effective length of query: 431 Effective length of database: 282 Effective search space: 121542 Effective search space used: 121542 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: 50 (23.9 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