Align Arogenate dehydratase 3; PhADT3; Prephenate dehydratase ADT3; EC 4.2.1.91; EC 4.2.1.51 (characterized)
to candidate HSERO_RS18430 HSERO_RS18430 chorismate mutase
Query= SwissProt::D3U717 (434 letters) >FitnessBrowser__HerbieS:HSERO_RS18430 Length = 357 Score = 155 bits (391), Expect = 2e-42 Identities = 109/317 (34%), Positives = 157/317 (49%), Gaps = 38/317 (11%) Query: 128 DLSPAPMHGAQLR------------------VAYQGVPGAYSEAAAGKAYPKC-EAIPCD 168 D +P P+ GA ++ VAY G G +SE A + + E + C Sbjct: 60 DRNPGPLLGADIQTIFREVMSACRALEKRVVVAYLGPEGTFSEQAVYQQFGHAIEGLSCV 119 Query: 169 QFEVAFQAVELWIADRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPG 228 + F+ E AD V+PIENS G I+R DLLL+ L I GEV +PVHH L+ G Sbjct: 120 SIDEVFRDAEAGTADFGVVPIENSSEGVINRTLDLLLQTTLTISGEVSIPVHHSLMTASG 179 Query: 229 VRKEYLTRVISHPQALAQCELTLTKLGLNVAREAVDDTAGAAEYIAANNLRDTAAIASSR 288 + E +TR+ +H QALAQC L + ++ R+AV A AA A + AAIA Sbjct: 180 -KMEGITRICAHSQALAQCNAWLNQNYPSIERQAVASNAEAAR--MAGEDQSVAAIAGEI 236 Query: 289 AAELYGLDILEQGIQDDLSNVTRFVMLAREPIIPRTDRPFKTSIVFAHDKGTSVLFKVLS 348 A + Y L + IQDD N TRF ++ R P +TSIV + ++ +L+ Sbjct: 237 AGQKYNLQTVNAHIQDDPHNRTRFAVIGRLRTAP--SGRDQTSIVLSVPNKAGAVYNLLA 294 Query: 349 AFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYVDFEASMADVRAQNALAEV 408 A +S+T+ ESRP A +G +EY FYVD E D + AL E+ Sbjct: 295 PLARHGVSMTRFESRP-----------ARMGA---WEYYFYVDLEGHEQDEKVAQALEEL 340 Query: 409 QEFTSFLRVLGSYPMDM 425 ++ +F ++LGSYP+ + Sbjct: 341 RQNAAFFKLLGSYPLGL 357 Lambda K H 0.319 0.132 0.383 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: 316 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: 434 Length of database: 357 Length adjustment: 31 Effective length of query: 403 Effective length of database: 326 Effective search space: 131378 Effective search space used: 131378 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 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