Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Pf6N2E2_6056 Para-aminobenzoate synthase, aminase component (EC 2.6.1.85)
Query= curated2:P05378 (462 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6056 Length = 447 Score = 246 bits (627), Expect = 1e-69 Identities = 151/362 (41%), Positives = 202/362 (55%), Gaps = 5/362 (1%) Query: 96 PFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFVEPEVVAVFDHLKNLLHLVAPGRD 155 PF GGV+GY +YD R+ E LPS DDL LPD F + V DH LV Sbjct: 88 PFAGGVIGYLSYDFGRHLETLPSHAKDDLQLPDARFGVYDWALVSDHQAGTSQLVFHPHC 147 Query: 156 PEEAEARLFWAERRLKGPLPGVPGERAGGRARFQADFSREAYLEAVRRALDYIRAGDIFQ 215 E+ RL + GV D S EAY +A R YI+AGD +Q Sbjct: 148 GEDERQRLIALFSQPTAASVGV----FSLEGPMTPDLSAEAYRQAFERIQAYIQAGDCYQ 203 Query: 216 VVLSLRLSSPLTVHPFALYRALRSVNPSPYMGYLDLGEV-VLVSASPESLLRSDGRRVVT 274 V + R +P +A Y+ALR+ P+P+ G+ L + ++S SPE ++ +V T Sbjct: 204 VNFAQRFRAPCQGDAWAAYQALRAACPTPFSGFQSLPDGGAVLSLSPERFVKVSEGQVET 263 Query: 275 RPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHVMLLDLSRNDIGRVAAFGTVRVLEPLH 334 RPI GTRPRG ED A ELL K+ AE++M++DL RND+GR G+VRV E Sbjct: 264 RPIKGTRPRGTTPSEDAAHAAELLASPKDRAENLMIVDLLRNDLGRTCRIGSVRVPELFS 323 Query: 335 VEHYSHVMHLVSTVEGILAEGKTPLDALASVLPMGTVSGAPKIRAMEIIEELEPHRRGPY 394 +E Y +V HLVS+V G LA K LD +A P G+++GAPKIRAM+II+ELEP RRG Y Sbjct: 324 LESYPNVHHLVSSVTGELAVDKDALDLIAGSFPGGSITGAPKIRAMQIIDELEPTRRGLY 383 Query: 395 GGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAGAGIVADSVPEREYEECWNKARALLKA 454 GS YL G MD ++ +R+ +V G + G GIVADS + EY+E K + LL+ Sbjct: 384 CGSLLYLDVRGEMDSSIAIRSLLVKDGQVCCWGGGGIVADSDWQAEYQESITKVKVLLET 443 Query: 455 VE 456 ++ Sbjct: 444 LQ 445 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: 505 Number of extensions: 18 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: 447 Length adjustment: 33 Effective length of query: 429 Effective length of database: 414 Effective search space: 177606 Effective search space used: 177606 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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