Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate BWI76_RS14505 BWI76_RS14505 salicylate synthase Irp9
Query= BRENDA::Q06128 (421 letters) >FitnessBrowser__Koxy:BWI76_RS14505 Length = 436 Score = 142 bits (358), Expect = 2e-38 Identities = 104/322 (32%), Positives = 160/322 (49%), Gaps = 17/322 (5%) Query: 104 AEDWPYAEFFTPDNIIIYDHNEGKVYVNADLSSVGGCGDIGEFKVSF----------YDE 153 A +WP P +I++ +G V V AD S GC + E+ D Sbjct: 113 AGEWPLLTLTAPREELIFE--KGNVTVYAD--SADGCRRLCEWVKEVDTATPCGPMVVDT 168 Query: 154 SLNKNSYERIVSESLEYIRSGYIFQVVLSRFYRYIFSGD-PLRIYYNLRRINPSPYMFYL 212 +L+ +Y++ V+ ++ I G +V++SR D P + Y R+ N F Sbjct: 169 ALDGEAYKQQVARAVSAIHRGDYVKVIVSRAIPLPARIDMPATLLYG-RQANTPTRSFMF 227 Query: 213 KFDEKYLIGSSPELLFRVQDNIVETYPIAGTRPRGADQEEDLKLELELMNSEKDKAEHLM 272 + + +G SPEL+ V N V T P+AGTR R D + E EL++ K+ EH++ Sbjct: 228 RQQGREALGFSPELVMSVTGNKVVTEPLAGTRDRMGDTAHNQANERELLHDGKEVLEHIL 287 Query: 273 LVDLARNDLGKVCVPGTVKVPELMYVEKYSHVQHIVSKVIGTLKKKYNALNVLSATFPAG 332 V A +L VC PG+V V +LM V + VQH+ S V G L + +A + + FP+ Sbjct: 288 SVKEAIAELEAVCQPGSVVVEDLMSVRQRGSVQHLGSGVSGQLAEDKDAWDAFTVLFPSI 347 Query: 333 TVSGAPKPMAMNIIETLEEYKRGPYAGAVGFISADGNAEFAIAIRTAFLNKELLRIHAGA 392 T SG PK A+N I +E+ R Y+GA+ + D + A+ +R+ F + + I AGA Sbjct: 348 TASGIPKKAALNAIMQIEKTPRELYSGAI-LLLEDTRFDAALVLRSVFQDSQRCWIQAGA 406 Query: 393 GIVYDSNPESEYFETEHKLKAL 414 GI+ S PE E ET KL ++ Sbjct: 407 GIIAQSTPERELTETREKLASI 428 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: 343 Number of extensions: 15 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: 421 Length of database: 436 Length adjustment: 32 Effective length of query: 389 Effective length of database: 404 Effective search space: 157156 Effective search space used: 157156 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 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