Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate GFF2281 Psest_2326 aminodeoxychorismate synthase, component I, bacterial clade
Query= curated2:O66849 (494 letters) >FitnessBrowser__psRCH2:GFF2281 Length = 448 Score = 239 bits (611), Expect = 1e-67 Identities = 150/396 (37%), Positives = 220/396 (55%), Gaps = 31/396 (7%) Query: 99 KIKEVVKKFIPYHDERLPRFWGGLVGYFAYDVVKFYEPV----EDKNPDPIHTYDIY--L 152 K++E+ +P D LP F GGL+G +YD E + ED + P+ + +Y Sbjct: 72 KLRELGDAELP-DDSELP-FTGGLIGLLSYDFGSRLETLPQQAEDDSGLPLARFGLYDWA 129 Query: 153 VLTDVVVIHDNLTGKIKVVVPIFAQNGIEEEYERAKNLIRDTVKKLKERGTTFLNVVEKE 212 ++TD H T ++ +F E E ER +L V E Sbjct: 130 LITD----HQRQTSQL-----MFHPALAEPERERLIHLFDSAA------------VGESA 168 Query: 213 PD--FKNWRSNFTKEEFEDIVKKAKEYIAQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFL 270 P +R++ + + + +++ + YI GD QV +QRFR + G+ Y LR Sbjct: 169 PFRLLDRFRADLSIDAYRHGIERIQAYIQAGDCYQVNFTQRFRAGYSGDAWPAYCALREA 228 Query: 271 NPSPYMYYLDFDQLKVIGSSPEILVRLEEGRIETRPIAGTRKRGRTEEEDKRLEEDLLSD 330 P+PY ++ D + SPE +RL +G +ETRPI GTR RG E D + LL+ Sbjct: 229 CPTPYAGFVALDDGAIASLSPERFLRLHQGHVETRPIKGTRPRGGDEHSDAEQAQALLAS 288 Query: 331 EKERAEHLMLVDLARNDIGRVAKTGSVRVENFMRIERYSHVMHIVSDVVGELREGYDALD 390 EK+RAE+LM+VDL RND+GR + GSVRV +E Y +V H+VS V GEL + +DA D Sbjct: 289 EKDRAENLMIVDLLRNDLGRSCRIGSVRVPELFALESYPNVHHLVSCVTGELADHHDAFD 348 Query: 391 VLKATFPAGTVSGAPKVRAMQIIEELENERRGIYAGSVGYISFQGNMDMAIAIRTAVYRD 450 +L +FP G+++GAPK+RAMQII+ELE RR IY GS+ YI +G MD +IAIRT + D Sbjct: 349 LLAGSFPGGSITGAPKIRAMQIIDELEPTRRAIYCGSLLYIDVRGEMDSSIAIRTLLICD 408 Query: 451 RDIFVQAGAGIVADSVPEKEWEETVNKAKALMKAIE 486 + G GIVADS + E++E+++K K L++ +E Sbjct: 409 GQVSCWGGGGIVADSDWQAEYQESIDKVKVLLQTLE 444 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: 456 Number of extensions: 14 Number of successful extensions: 2 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: 448 Length adjustment: 33 Effective length of query: 461 Effective length of database: 415 Effective search space: 191315 Effective search space used: 191315 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