Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Ac3H11_3836 Para-aminobenzoate synthase, aminase component (EC 2.6.1.85) / Aminodeoxychorismate lyase (EC 4.1.3.38)
Query= curated2:Q9Y8T0 (438 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3836 Length = 610 Score = 154 bits (388), Expect = 1e-41 Identities = 109/308 (35%), Positives = 155/308 (50%), Gaps = 23/308 (7%) Query: 146 DTPLPAPASRKESFSAEGPTYET-----SRKGFEAMVADALERIRAGEAFQVVLSRVERY 200 D PLP PA + AE P T R F+A +A + I AGE +QV + Sbjct: 98 DAPLPWPAC-DDGQGAEPPAQVTWTDSPDRAPFDAALAQIQQAIAAGELYQVNHTAPLHG 156 Query: 201 RVWGSLFSAYERLADANPSPYLYYARLGGRVIIGSSPELLVKLE----AGRVETHPIAGT 256 + G+ + + L A P Y + GG ++ SPEL G + P+ GT Sbjct: 157 TLQGAAPALFAALLRAQPGGYAAHIDTGGEQVLSVSPELFFDWRDAPGGGHILARPMKGT 216 Query: 257 RPRGSTPIEDIELEVELLNDEKERAEHVMLVDLARNDITRVSIPGTVQVTSFMDIERYET 316 PRG+TP ED + V L KERAE+VM+VDL RND++R++ P +V+V + T Sbjct: 217 APRGATPEEDAQQAVHLRTAPKERAENVMIVDLLRNDVSRIAQPHSVRVPVLFATQALPT 276 Query: 317 VMHIVSRVEGVTRPSTTFVEALKALHPAGTVSGAPKPRAMEIIAELEEEARGPYAGAIGV 376 V + S V TRP TT + AL P G+V+GAPK RAM++I LE RG Y GA+GV Sbjct: 277 VWQMTSDVTARTRPGTTLTDVFAALFPCGSVTGAPKVRAMQMIHALEGAPRGVYCGAVGV 336 Query: 377 ---AG--SSAGEAAIV------LRSAWLLDDGETLEARA--GAGIVYDSKPEREYMETVQ 423 AG + G+ A+ +R+ L +G T+ A G+GI + + E+ E Sbjct: 337 VRPAGPPDAQGQHAVAATFNVPIRTVVLRPEGGTVHATCGIGSGITSGALADAEWSEWQH 396 Query: 424 KLGSLKRA 431 K ++RA Sbjct: 397 KRAFVERA 404 Lambda K H 0.317 0.135 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: 658 Number of extensions: 35 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: 438 Length of database: 610 Length adjustment: 35 Effective length of query: 403 Effective length of database: 575 Effective search space: 231725 Effective search space used: 231725 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 (21.6 bits) S2: 52 (24.6 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