Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate HSERO_RS07665 HSERO_RS07665 anthranilate synthase
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__HerbieS:HSERO_RS07665 Length = 615 Score = 83.2 bits (204), Expect = 2e-20 Identities = 102/354 (28%), Positives = 152/354 (42%), Gaps = 32/354 (9%) Query: 111 AFEFGVHRYGLQQRLAPHTPLARV--FSPRTRIMVSEKEIRLFDAGIRHREAIDRLLATG 168 ++E G GL PLARV F+ R+ +E + L A + D + G Sbjct: 60 SYELGAALQGLPHHRL-QGPLARVLLFAHCERLAATEVDTWL--AASCQADGADMFTSGG 116 Query: 169 VREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAID-FPLTYRLG 227 + + S D + F +A D IAAG ++V + + D L RL Sbjct: 117 IANLRSSV------DEAAFSAAIARIRDYIAAGDTYQVNYTYRLHGDVHGDAIGLYRRLR 170 Query: 228 RRHNTPVRSFLL-QLGGIRALGYSPELVTAVRADGVVITEPLAGT-RALGR----GPAID 281 R P + + +LGG+ L SPEL + GV+ +P+ GT RAL ++ Sbjct: 171 ARQPVPYGALVRDELGGM-VLSCSPELFVS-HQQGVLKAKPMKGTARALPPEQEGAETVN 228 Query: 282 RLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRA 341 L ++ K E+ + V ++ +A PGS V VR G V + STIRA Sbjct: 229 AQRALALAADEKNRAENLMIVDLLRNDLGRVAVPGSVQVPHLFDVRRYGQVLQMTSTIRA 288 Query: 342 RLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSA--DGGLD 399 RL + + AL+P + +G PK +E I L+ PRGLY+GA+ A GG Sbjct: 289 RLREHATLADTINALYPCGSITGAPKRRTMEIIHELESEPRGLYTGAIGWFDAPRPGGPA 348 Query: 400 ----------AALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEKLSTLT 443 L L+A + + + GAGI+ +S+ EF E K S LT Sbjct: 349 IGDFCLSVPIRTLELQAPHAGLRKAVMGVGAGIVHDSQAAAEFAECQLKSSFLT 402 Lambda K H 0.319 0.135 0.386 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: 600 Number of extensions: 32 Number of successful extensions: 1 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: 450 Length of database: 615 Length adjustment: 35 Effective length of query: 415 Effective length of database: 580 Effective search space: 240700 Effective search space used: 240700 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: 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