Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate WP_035241586.1 Q366_RS17620 bifunctional chorismate mutase/prephenate dehydrogenase
Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER (373 letters) >NCBI__GCF_000745975.1:WP_035241586.1 Length = 380 Score = 323 bits (828), Expect = 5e-93 Identities = 161/365 (44%), Positives = 236/365 (64%), Gaps = 1/365 (0%) Query: 4 ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAEA 63 ++ +RD+ID +D +++LL+KR E V ++ VK +PIY P RE +++ R +A Sbjct: 11 QIKPIRDEIDAIDARIISLLSKRREQVEKIVAVKKEHKVPIYHPAREEDVISRLRGKASD 70 Query: 64 LGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSGY 123 + V PDL+E++ R +M +S S+ +L +++VGG G+MGRLF + T +GY Sbjct: 71 MDVDPDLVENLYRTIMHQSRKSQTRVSKTSLIRPQARILVVGGAGEMGRLFVRFFTDTGY 130 Query: 124 QVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIGKLPPLPK-DCILVDLASVKNGPL 182 V IL++ DWDRA + +A +VIV VPI+VT +VI L PL + D +L DL SVK PL Sbjct: 131 PVDILDKDDWDRAQALCKNADLVIVCVPINVTVKVIDALAPLMRPDAVLTDLTSVKTLPL 190 Query: 183 QAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRISA 242 +AM AH GPVLGLHP+FGP + +L KQ++ C G+K +A QW ++Q+ WGA + SA Sbjct: 191 EAMCRAHTGPVLGLHPLFGPTTNNLDKQIIAACSGQKDDACQWVIDQLVAWGAVVVETSA 250 Query: 243 VEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQL 302 EHDQ M +QALRHFATF++G L + + +++ L SSPIYRLEL MVGRLFAQDP L Sbjct: 251 REHDQVMEIVQALRHFATFSFGSFLYRQGIPIKRTLEFSSPIYRLELGMVGRLFAQDPDL 310 Query: 303 YADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSESR 362 YA+II ++ L+K + + + +++LE GDK AFI F ++ WFG + + ES Sbjct: 311 YAEIIFATPERRQLLKTFVQSLTQFLDMLESGDKDAFIKEFNQIAEWFGPFGNQALREST 370 Query: 363 VLLRQ 367 + + Sbjct: 371 YFINK 375 Lambda K H 0.322 0.138 0.404 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: 377 Number of extensions: 14 Number of successful extensions: 2 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: 373 Length of database: 380 Length adjustment: 30 Effective length of query: 343 Effective length of database: 350 Effective search space: 120050 Effective search space used: 120050 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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