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 N515DRAFT_1431 N515DRAFT_1431 chorismate mutase
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__Dyella79:N515DRAFT_1431 Length = 362 Score = 172 bits (435), Expect = 3e-47 Identities = 119/342 (34%), Positives = 181/342 (52%), Gaps = 18/342 (5%) Query: 260 TKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEE----KL 315 T+ S+E++R I SID I LI R A+++AR+K I+ E E ++ Sbjct: 2 TEPKASLEQVRERIDSIDRQIQELISERAGWAQEVARVKGAGLSAIDYYRPEREAHVLRM 61 Query: 316 WEVMSKTTLNPVKLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVG 373 ++ L+ ++ +F IMS LA+E+ KV LGP+G+FSE+ K G Sbjct: 62 VVDRNRGPLSDTEMVRLFREIMSSCLAQEDPLKVG-------FLGPEGTFSEQAVRKHFG 114 Query: 374 SRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEV 433 + +E+ + V +G D+G+VP+ENS G + +D L + + GE +L V Sbjct: 115 HAAYGLPLGSIEEVFQEVAAGHADFGVVPVENSGQGMIQITLDMFLTSEATICGEIELRV 174 Query: 434 NHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYS 491 + CL ++ +++IK +Y+H Q++ QC ++ LP V +S ++AARM D + Sbjct: 175 HQCLHSQGG-RMEDIKRVYAHAQSLQQCKTWLRINLPDVECIAVSSNAEAARMARHADDA 233 Query: 492 AAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGA 550 AAI E A R Y L L GI+D + N TRF +I R G TSL V DKPGA Sbjct: 234 AAIAGETAGRVYGLKTLATGIED-RADNTTRFLVIGRSLFPPSGNDRTSLLITVNDKPGA 292 Query: 551 LKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLRE 592 L DVL F K +L ++ESRPA TG Y FF++V +++ Sbjct: 293 LYDVLSPFAKHDVSLNRIESRPAHTGKWQYAFFIDVSGHVQD 334 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: 408 Number of extensions: 14 Number of successful extensions: 5 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: 362 Length adjustment: 33 Effective length of query: 587 Effective length of database: 329 Effective search space: 193123 Effective search space used: 193123 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: 51 (24.3 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