Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_013075896.1 BTUS_RS09570 anthranilate synthase component I family protein
Query= BRENDA::P9WFX1 (450 letters) >NCBI__GCF_000092905.1:WP_013075896.1 Length = 485 Score = 136 bits (342), Expect = 2e-36 Identities = 126/411 (30%), Positives = 194/411 (47%), Gaps = 38/411 (9%) Query: 59 GVQAMVELDSDELRVIRDGVTRRQQWSGRPGAALGEA------VDRLLLETDQAFGWVAF 112 G +A+V D+ + R+ ++ + + +G P L V+ L G+VA+ Sbjct: 79 GDEALV--DAVKRRLAQERLVEGSEIAGDPAEVLAAVSGVFAPVEDLPAFAGGFLGYVAY 136 Query: 113 EFGVHRYGLQQRLAPHTPLARVFSPRTRIMVSEKEIRLFDAGIR---HR-----EAIDRL 164 + RY +RL PHT + R+ V + + D G+ HR + +DR+ Sbjct: 137 D--AIRYF--ERL-PHTTVDDRQLDDIRLQVHRSVVHVTDEGLEVFAHRFGEADDDLDRV 191 Query: 165 L-----ATGVREVPQ------SRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVE 213 L A + ++P+ S DV+++ F RRV A + IA G +++ S ++ Sbjct: 192 LGWIDRADRLPDLPRDVAPVLSVKQDVTEEE--FVRRVEKAKNYIADGDIFQIVPSMRIQ 249 Query: 214 VPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRA 273 V A D + Y RR N F G R G SPE+ V+ DGV P+AGT + Sbjct: 250 VNSAADPLVVYDRLRRCNPSPFMFYADYGDSRIFGASPEVQLRVQ-DGVAQMRPIAGT-S 307 Query: 274 LGRGPAIDRLAR--DDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGS 331 G+G + R +DL + KE EH + V ++ + PG+ V M V E Sbjct: 308 KGKGKTAEENRRLVEDLLGDEKERAEHLMLVDLCRNDLGRVCRPGTVVVEQLMVVEEYSH 367 Query: 332 VQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVM 391 V H+ S +R L P + A+ A FPA T SG PK +E I L+ RG Y GAV Sbjct: 368 VFHIVSHVRGELRPEVKPLQAILATFPAGTLSGTPKVRAMEIIDELESFDRGPYGGAVGF 427 Query: 392 LSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEKLSTL 442 + G ++ A+ +R+ QVG +L+AGAGI+ +S PE E+ E KL+ L Sbjct: 428 IDWRGNVNLAIMIRSVVQVGDVFYLQAGAGIVADSVPEMEWRECGHKLAAL 478 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: 470 Number of extensions: 28 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: 485 Length adjustment: 33 Effective length of query: 417 Effective length of database: 452 Effective search space: 188484 Effective search space used: 188484 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 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