Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate BWI76_RS21475 BWI76_RS21475 bifunctional chorismate mutase/prephenate dehydrogenase
Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER (373 letters) >FitnessBrowser__Koxy:BWI76_RS21475 Length = 373 Score = 670 bits (1729), Expect = 0.0 Identities = 340/373 (91%), Positives = 353/373 (94%) Query: 1 MVAELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAE 60 MVAELTALRDQIDEVDKALL LLAKRLELVA+VGEVKS +GLPIYVPERE++MLASRR E Sbjct: 1 MVAELTALRDQIDEVDKALLELLAKRLELVAQVGEVKSHYGLPIYVPERESAMLASRREE 60 Query: 61 AEALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTL 120 A ALGVPPDLIEDVLRRVMRESYSSENDKGFKTL P+LRPVVIVGGGGQMGRLFEKMLTL Sbjct: 61 AAALGVPPDLIEDVLRRVMRESYSSENDKGFKTLYPNLRPVVIVGGGGQMGRLFEKMLTL 120 Query: 121 SGYQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIGKLPPLPKDCILVDLASVKNG 180 SGYQVRILE+ DW RA +IVADAGMVIVSVPIH+T I +LPPLP DCILVDLASVK Sbjct: 121 SGYQVRILEKDDWSRADEIVADAGMVIVSVPIHITAATIAQLPPLPADCILVDLASVKAE 180 Query: 181 PLQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRI 240 PLQAML AH GPVLGLHPMFGPDSGSLAKQVVV+CDGR+PEAYQWFLEQIQVWGARLHRI Sbjct: 181 PLQAMLAAHKGPVLGLHPMFGPDSGSLAKQVVVYCDGRQPEAYQWFLEQIQVWGARLHRI 240 Query: 241 SAVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDP 300 SAVEHDQNMAFIQALRHFATFAYGLHLAEENV+LEQLLALSSPIYRLELAMVGRLFAQDP Sbjct: 241 SAVEHDQNMAFIQALRHFATFAYGLHLAEENVRLEQLLALSSPIYRLELAMVGRLFAQDP 300 Query: 301 QLYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE 360 QLYADIIMSSE NLALIKRYY+RFGEAI LLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE Sbjct: 301 QLYADIIMSSENNLALIKRYYQRFGEAIGLLEQGDKQAFIDSFRKVEHWFGDYAQRFQSE 360 Query: 361 SRVLLRQANDNRQ 373 SR LLRQANDNRQ Sbjct: 361 SRTLLRQANDNRQ 373 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: 545 Number of extensions: 13 Number of successful extensions: 1 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: 373 Length adjustment: 30 Effective length of query: 343 Effective length of database: 343 Effective search space: 117649 Effective search space used: 117649 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 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