Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); Chorismate mutase (EC 5.4.99.5) (characterized)
to candidate RR42_RS04460 RR42_RS04460 chorismate mutase
Query= BRENDA::O30012 (620 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS04460 RR42_RS04460 chorismate mutase Length = 379 Score = 165 bits (418), Expect = 3e-45 Identities = 115/364 (31%), Positives = 191/364 (52%), Gaps = 18/364 (4%) Query: 259 ATKKAESIE--ELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLW 316 A +KA +E LR I ++D +L ++ RR A + +K + G P+ + E + + Sbjct: 19 AAEKALGVELTPLREQIDTLDRELLAMLNRRAQLALDVGEVKKKYGAPVFRPERELQVIR 78 Query: 317 EVMSKTTLNPVKLKEIFEGIMSLAKEEEYKVAGVK--YTIAVLGPQGSFSEEMALKLVGS 374 +V NP L + + + ++ +E G++ +A LGP G+FSE+ G Sbjct: 79 KVQGA---NPGPLLD--DSVAAIWREVMSACRGLEKPLEVAFLGPAGTFSEQALYAHFGH 133 Query: 375 RVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVN 434 V C + DE+ + VE+G V+YG+VP+ENS G V +D L +++ GE L+V+ Sbjct: 134 EVSGVPCPSIDEVFRAVEAGTVEYGVVPVENSTEGAVSRTLDLFLQTSLKISGEIALKVH 193 Query: 435 HCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSA 492 H L+A ++K + + +H QA+AQC ++ P + + +S ++AARM D A Sbjct: 194 HNLMASSP-DMKGVTVVRAHAQALAQCQHWLTANYPHLERQAVSSNAEAARMASEDPTVA 252 Query: 493 AIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGAL 551 AI E+AA Y LH++R IQD N TRF +I R G TS+ V +K GA+ Sbjct: 253 AIAGESAANRYHLHLVRTHIQD-DPHNRTRFAVIGRYETEPSGSDQTSMILSVPNKAGAV 311 Query: 552 KDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKV 607 +L G ++ + ESRPA +G +Y F+V+VE + L +L++ ++KV Sbjct: 312 YQLLAPLADNGVSMCRFESRPARSGAWEYYFYVDVEGHQHDASVARALEELRRNAAYFKV 371 Query: 608 VGVF 611 +G + Sbjct: 372 LGSY 375 Lambda K H 0.320 0.137 0.380 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: 391 Number of extensions: 23 Number of successful extensions: 4 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: 620 Length of database: 379 Length adjustment: 34 Effective length of query: 586 Effective length of database: 345 Effective search space: 202170 Effective search space used: 202170 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: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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