Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Echvi_2333 Echvi_2333 Anthranilate/para-aminobenzoate synthases component I
Query= curated2:P05378 (462 letters) >FitnessBrowser__Cola:Echvi_2333 Length = 413 Score = 192 bits (488), Expect = 2e-53 Identities = 112/362 (30%), Positives = 190/362 (52%), Gaps = 17/362 (4%) Query: 93 DLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVVAVFDHLKNLLHLVAP 152 D+ G G +YDL +ERL S P + P+ F PE+ +F + AP Sbjct: 60 DMDAHSGPKAGILSYDLKNKFERLKSQNPSLVNCPETCFFLPELTILFHEKTLEIKSAAP 119 Query: 153 GRDPEEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSREAYLEAVRRALDYIRAGD 212 R EE ++ P + ++ A Q S+ Y++ VR ++IR GD Sbjct: 120 DRLFEE-----------IRDYQPEIVSQKI---APVQVKTSKSEYIQTVRNIQEHIRQGD 165 Query: 213 IFQVVLSLRLSSPL-TVHPFALYRALRSVNPSPYMGYLDLGEVVLVSASPESLLRSDGRR 271 I+++ + + + +++P ++ L +P P+ + + LV ASPE ++ G + Sbjct: 166 IYEMNYCIAFEAVVESINPVQVFLDLEKKSPMPFASFFKCQDQYLVGASPERFIKKQGLQ 225 Query: 272 VVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLSRNDIGRVAAFGTVRVLE 331 + +PI GT RGK EED E L EKE AE++M++DL RND+ R+A G+++V E Sbjct: 226 ITAQPIKGTIQRGKTAEEDANYRESLRLSEKEQAENLMIVDLMRNDLARIAETGSIKVEE 285 Query: 332 PLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGAPKIRAMEIIEELEPHRR 391 + + V ++STV L G + + +A+ PMG+++GAPKI+ ME+I+ E +R Sbjct: 286 LFGIYPFRQVYQMISTVTATLRPGTSFTEIIANTFPMGSMTGAPKIKCMELIDRYENFKR 345 Query: 392 GPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHV--QAGAGIVADSVPEREYEECWNKAR 449 G + G+ G++ G +D ++ +R+ ++ H+ AG+ I D+ P EYEEC KA+ Sbjct: 346 GWFSGALGFVDEFGNLDFSVVIRSIIIDTKSKHLFFAAGSAITFDADPAYEYEECLLKAK 405 Query: 450 AL 451 A+ Sbjct: 406 AI 407 Lambda K H 0.321 0.139 0.408 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: 387 Number of extensions: 17 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: 462 Length of database: 413 Length adjustment: 32 Effective length of query: 430 Effective length of database: 381 Effective search space: 163830 Effective search space used: 163830 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 (21.8 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