Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_014026579.1 PYRFU_RS05145 anthranilate synthase component I
Query= BRENDA::Q06128 (421 letters) >NCBI__GCF_000223395.1:WP_014026579.1 Length = 437 Score = 316 bits (810), Expect = 8e-91 Identities = 183/425 (43%), Positives = 254/425 (59%), Gaps = 18/425 (4%) Query: 5 PISEFASPFEVFKCIERDFKVAGLLESIGGPQYKARYSVIAWSTNGYLKIHD--DPVNIL 62 P++ P + E+ + LLES G +ARY+++A N + D D N+L Sbjct: 21 PLARIPEPRRLVAWAEKRYDYVALLESGEGFPERARYTLVAMGANRVYETDDILDGFNVL 80 Query: 63 NGYLKDLKLADIPGLFKGGMIGYISYDAVRFWEKIRDLKPAAEDWPYAEFFTPDNIIIYD 122 L+ +P + + G +SY+AV E K WP F P+ +++YD Sbjct: 81 WKALRGRGCDALP--CRSMLFGVVSYEAVAGVEPWLAPKLRRHTWPVVRVFEPEVLVVYD 138 Query: 123 HNEGKVYVNADLSSVGGCGDIGEFKVSFYDESLN------KNSYERIVSESLEYIRSGYI 176 G+ YV G D+GE ++ + ++ + +E V E+ I G Sbjct: 139 RLTGRAYV------CPGDADLGEAEIGGFVQARGPVYETPREEFEAWVREAKRLIEEGEF 192 Query: 177 FQVVLSRFYRYIFSGDPLRIYYNLRRINPSPYMFYLKFDEKYLIGSSPELLFRVQDNIVE 236 FQ+VLSR RY ++G PL +Y L NPSPYMFYL+ + +++G+SPELL ++ E Sbjct: 193 FQIVLSRVERYEYNGSPLALYERLAGGNPSPYMFYLRMGDHWIVGTSPELLVKMSLGRAE 252 Query: 237 TYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLMLVDLARNDLGKVCVPGTVKVPELM 296 T+PIAGTRPRG EED+ LE E++ EK++AEH+MLVDLARNDLG++ VPGTV+V LM Sbjct: 253 THPIAGTRPRGKTPEEDVALEEEMLRDEKERAEHMMLVDLARNDLGRIAVPGTVRVTALM 312 Query: 297 YVEKYSHVQHIVSKVIGTLKKKYNALNVLSATFPAGTVSGAPKPMAMNIIETLEEYKRGP 356 VEKYSHVQH+VS+V +K K +VL+ATFPAGTVSGAPK AM I LE+ RGP Sbjct: 313 DVEKYSHVQHLVSRVEALVKPKTLYSDVLAATFPAGTVSGAPKTRAMEYIAVLEDEPRGP 372 Query: 357 YAGAVGFISADGNAEFAIAIRTAFLNKE-LLRIHAGAGIVYDSNPESEYFETEHKLKALK 415 YAGAVG + A+ E AI IR+ + ++ ++ AGAGIVYDS PE EY ET HK+ A++ Sbjct: 373 YAGAVG-VYAERAGETAIVIRSVWSYEDGIVEARAGAGIVYDSVPEREYMETVHKIMAVR 431 Query: 416 TAIGV 420 A+GV Sbjct: 432 RALGV 436 Lambda K H 0.319 0.139 0.410 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: 535 Number of extensions: 25 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: 421 Length of database: 437 Length adjustment: 32 Effective length of query: 389 Effective length of database: 405 Effective search space: 157545 Effective search space used: 157545 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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