Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_077243791.1 B1A74_RS03675 aminodeoxychorismate synthase component I
Query= curated2:O66849 (494 letters) >NCBI__GCF_001995255.1:WP_077243791.1 Length = 451 Score = 236 bits (602), Expect = 1e-66 Identities = 133/264 (50%), Positives = 171/264 (64%), Gaps = 3/264 (1%) Query: 225 EEFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDN--IYRVLRFLNPSPYMYYLDFD 282 E + V+ A EYI GD Q LS+ + R + D +YR LR N +P+ +L Sbjct: 180 EYYRAAVRGALEYIRAGDTFQANLSREWHARADRSLDTGELYRRLRGANAAPFAAWLRLP 239 Query: 283 QLKVIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEHLMLVD 342 +VI SSPE LV +EG ETRPIAGTR+R D+ L +L + KERAEH+MLVD Sbjct: 240 GAEVISSSPERLVSAQEGVAETRPIAGTRRRDPDAHADRELYGELEVNLKERAEHIMLVD 299 Query: 343 LARNDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFPAGTVS 402 L RND+GRVA TGSVRV M IE Y V HIVS + LR G A ++L++TFP GT++ Sbjct: 300 LERNDLGRVACTGSVRVAELMTIESYRRVHHIVSSITARLRPGTRAEELLRSTFPGGTIT 359 Query: 403 GAPKVRAMQIIEELENE-RRGIYAGSVGYISFQGNMDMAIAIRTAVYRDRDIFVQAGAGI 461 G PK+R+MQ+I+ELE RG Y GS GY+S G MD I IRT V RDR++ +AGAGI Sbjct: 360 GCPKIRSMQVIQELEGRVPRGAYTGSCGYVSDHGRMDTNILIRTLVVRDRELRFRAGAGI 419 Query: 462 VADSVPEKEWEETVNKAKALMKAI 485 VADS P++E EET +KA+ L+ A+ Sbjct: 420 VADSDPDQELEETRHKARGLLDAL 443 Lambda K H 0.318 0.138 0.390 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: 467 Number of extensions: 22 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: 494 Length of database: 451 Length adjustment: 33 Effective length of query: 461 Effective length of database: 418 Effective search space: 192698 Effective search space used: 192698 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 09 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