Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_011841694.1 RSPH17029_RS12485 aminodeoxychorismate synthase component I
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000015985.1:WP_011841694.1 Length = 381 Score = 95.5 bits (236), Expect = 3e-24 Identities = 113/375 (30%), Positives = 152/375 (40%), Gaps = 60/375 (16%) Query: 90 AALGEAVDRLLLETDQAF---GWVAFEFGVHRYGLQQRLAPHTPLARVFSPR-TRIMVSE 145 AAL A+ RL + F G VA+E G+ VF PR R+M + Sbjct: 28 AALAPALARLDALRAEGFWIAGTVAYEAGL-----------------VFEPRLARLMPPQ 70 Query: 146 KEIRLFDAG-IRHREAIDRLLATGVREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYH 204 + L G R LLA E + R FR R+A A + A GR Sbjct: 71 RSEPLLAFGAFRAPLPAGDLLAQAAAEAGEVRLAP-------FRPRIARADYDAAFGRLM 123 Query: 205 KVILSR-CVEVPFAIDFPLTYRL----------GRRHNTPV-RSFLLQLGGIRALGYSPE 252 I + C +V + FPL RL R PV + LGG A+ SPE Sbjct: 124 AYIAAGDCYQVN--LTFPLDGRLEAGSALGLYGALRARQPVGQGAFCDLGGPVAISASPE 181 Query: 253 LVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDI 312 L A+G + T P+ GT PA D L S+ K E+ + V +I I Sbjct: 182 LFFDCDAEGRISTRPMKGTAPRDPDPARDAELAKILGSSEKGRAENLMIVDLLRNDIGRI 241 Query: 313 AEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVE 372 AE GS V + + +V + S + RL L ALFP + +G PK +E Sbjct: 242 AELGSVRVPELFAIESYATVHQMVSRVTGRLIGWPGLSGLLPALFPCGSVTGAPKIRAME 301 Query: 373 AIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQV---------GGRTWLRAGAGII 423 I L+ PRGLY GA+ ++ DG RAA+ V GG L G GI+ Sbjct: 302 IIGELEPFPRGLYCGAMGWMAPDG--------RAAFNVAIRTLRLFPGGELRLDVGGGIV 353 Query: 424 EESEPEREFEETCEK 438 ++S E+EE K Sbjct: 354 QDSTAPGEWEEALWK 368 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: 435 Number of extensions: 22 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: 450 Length of database: 381 Length adjustment: 31 Effective length of query: 419 Effective length of database: 350 Effective search space: 146650 Effective search space used: 146650 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: 50 (23.9 bits)
This GapMind analysis is from Apr 16 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