Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate N515DRAFT_1431 N515DRAFT_1431 chorismate mutase
Query= BRENDA::Q9SGD6 (413 letters) >FitnessBrowser__Dyella79:N515DRAFT_1431 Length = 362 Score = 143 bits (360), Expect = 9e-39 Identities = 115/348 (33%), Positives = 160/348 (45%), Gaps = 31/348 (8%) Query: 65 GHNSAAARVPGMNLVPIE------KSDSNPLVPQHRHNPLKPLSMTDL-----SPAPMHG 113 G ARV G L I+ ++ +V PL M L S Sbjct: 31 GWAQEVARVKGAGLSAIDYYRPEREAHVLRMVVDRNRGPLSDTEMVRLFREIMSSCLAQE 90 Query: 114 SNLRVAYQGVPGAYSEAAAGKAYPNCQ-AIPCDQFEVAFQAVELWIADRAVLPVENSLGG 172 L+V + G G +SE A K + + +P E FQ V AD V+PVENS G Sbjct: 91 DPLKVGFLGPEGTFSEQAVRKHFGHAAYGLPLGSIEEVFQEVAAGHADFGVVPVENSGQG 150 Query: 173 SIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEFLTRVISHPQGLAQCEHTLTKLG 232 I D+ L I GE++L VH CL + G R E + RV +H Q L QC+ L Sbjct: 151 MIQITLDMFLTSEATICGEIELRVHQCLHS-QGGRMEDIKRVYAHAQSLQQCKTWLRINL 209 Query: 233 LNVAREAVDDTAGAAEFIASNNLRDTAAIASARAAEIYGLEILEDGIQDDVSNVTRFVML 292 +V AV A AA + + D AAIA A +YGL+ L GI+D N TRF+++ Sbjct: 210 PDVECIAVSSNAEAARM--ARHADDAAAIAGETAGRVYGLKTLATGIEDRADNTTRFLVI 267 Query: 293 AREPIIPRTDRPFKTSIVFAHEKGTSVLFKVLSAFAFRDISLTKIESRPNHNRPIRVVDD 352 R P + +TS++ L+ VLS FA D+SL +IESRP H Sbjct: 268 GRSLFPPSGND--RTSLLITVNDKPGALYDVLSPFAKHDVSLNRIESRPAH--------- 316 Query: 353 ANVGTAKHFEYMFYVDFEASMAEARAQNALAEVQEFTSFLRVLGSYPM 400 T K ++Y F++D + +A Q A+ E+ + +RVLGSYP+ Sbjct: 317 ----TGK-WQYAFFIDVSGHVQDAPIQAAMQEMGGAAAQVRVLGSYPV 359 Lambda K H 0.317 0.131 0.381 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: 302 Number of extensions: 15 Number of successful extensions: 5 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: 413 Length of database: 362 Length adjustment: 30 Effective length of query: 383 Effective length of database: 332 Effective search space: 127156 Effective search space used: 127156 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: 50 (23.9 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