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) >FitnessBrowser__Cup4G11:RR42_RS04460 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 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