Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate H281DRAFT_04702 H281DRAFT_04702 para-aminobenzoate synthetase / 4-amino-4-deoxychorismate lyase
Query= curated2:Q9HS66 (488 letters) >FitnessBrowser__Burk376:H281DRAFT_04702 Length = 629 Score = 180 bits (456), Expect = 1e-49 Identities = 122/302 (40%), Positives = 161/302 (53%), Gaps = 20/302 (6%) Query: 187 RDGDPAVGPPPADSPAPFESVAGRAAFESRVRRIQDAIRDGDTFQANVSHRLDAPAAVHP 246 +DGD A P A + ESV A F + + I A+RDG+++Q N ++RL P Sbjct: 113 QDGDLAE-PSVAGTANVRESVEP-AEFNAAIGAIHAALRDGESYQVNYTYRLGFDVFGSP 170 Query: 247 VAVFEALRDTNPAPYSGIVEFPGVDLV-SASPELLLARRGRELTTEPIAGTRPRGATPAE 305 +A++ LR P Y ++ PG V S SPEL + ++ L P+ GT PR A P+ Sbjct: 171 IALYRRLRARQPVRYGALIAMPGNGWVLSCSPELFVEKQNATLRARPMKGTAPRSADPSA 230 Query: 306 DDAARAALRADDKERAEHAMLVDLERNDLGKVSEYGSVAVPDYRRVDAYSEVLHLVSEVT 365 D A L D K RAE+ M+VDL RNDL +V++ GSV VP V+ Y+ V + S V Sbjct: 231 DRGAAEFLGNDPKNRAENVMIVDLLRNDLSRVAQTGSVKVPALFSVEPYASVWQMTSTVE 290 Query: 366 GRLRDSCSLRDAIAAVFPGGTITGAPKPRTMALIDTVEATRRGPYTGSL----------- 414 LR S + A+FP G+ITGAPK RTM LID +E+T RG YTG++ Sbjct: 291 AALRPGTSFAAIVRALFPCGSITGAPKHRTMQLIDELESTPRGLYTGAIGWLDAPVLEPA 350 Query: 415 AAIGFDGDATLSITIRTLVRR--AATYHLR----VGAGIVHDSTPAAEYDETLAKARALV 468 A GD +S+ IRTL + A T LR +GAGIV DS EY E KAR L Sbjct: 351 ANENSGGDFCMSVAIRTLTLKPLAPTGELRGTMGIGAGIVLDSVAEDEYAECRLKARFLT 410 Query: 469 TA 470 A Sbjct: 411 GA 412 Lambda K H 0.317 0.135 0.397 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: 689 Number of extensions: 41 Number of successful extensions: 3 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: 488 Length of database: 629 Length adjustment: 36 Effective length of query: 452 Effective length of database: 593 Effective search space: 268036 Effective search space used: 268036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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