Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 7025863 Shewana3_3012 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)
Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER (373 letters) >FitnessBrowser__ANA3:7025863 Length = 379 Score = 423 bits (1088), Expect = e-123 Identities = 212/368 (57%), Positives = 270/368 (73%), Gaps = 1/368 (0%) Query: 4 ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAEA 63 EL LR ID VD+ LL+LL KRL+LVA+VG VK GLPIY P+REA+MLA RR EA+ Sbjct: 8 ELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAKT 67 Query: 64 LGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSGY 123 +G+ P LIED+LRR+MRESY +E D GFK + L VVIVGG GQ+G LF++ML+LSGY Sbjct: 68 MGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLSLSGY 127 Query: 124 QVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGPL 182 QV++L++ DW +A + ADAG+V+V+VPI +T +I KL LP++CIL DL S+K P+ Sbjct: 128 QVKVLDKDDWQQAETLFADAGLVLVTVPIAITCDIIREKLTQLPQECILADLTSIKTEPM 187 Query: 183 QAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRISA 242 AML AH GPV+G HPMFGPD GSLAKQVVV C GR + YQW LEQI +WGAR+ Sbjct: 188 NAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGRGADKYQWLLEQIGIWGARIVEAEP 247 Query: 243 VEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQL 302 HD M +QA+RHF+TF YGL+L +E +E LL SSPIYRLELAMVGRLFAQ P+L Sbjct: 248 ERHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLQFSSPIYRLELAMVGRLFAQSPEL 307 Query: 303 YADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSESR 362 YADII + + + I Y + EA+ELL++GD+ AFI F+ V WFGD+A +FQ ESR Sbjct: 308 YADIIFAQQDSQHAIGDYLDNYREALELLKRGDRDAFISQFQTVAKWFGDFAPQFQRESR 367 Query: 363 VLLRQAND 370 ++L+ +D Sbjct: 368 MMLQSVSD 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: 390 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: 379 Length adjustment: 30 Effective length of query: 343 Effective length of database: 349 Effective search space: 119707 Effective search space used: 119707 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 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:
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