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 WP_019866292.1 METMI_RS0110720 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000384075.1:WP_019866292.1 Length = 361 Score = 174 bits (440), Expect = 8e-48 Identities = 116/331 (35%), Positives = 185/331 (55%), Gaps = 18/331 (5%) Query: 266 IEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLW----EVMSK 321 + ELR I ++D+ +LRL+ R A ++A+ K+ +GE + E L + +++ Sbjct: 7 LAELREKIDALDAEVLRLLNERAKCAMEVAKTKIAQGEVGTFYRPDRESLVLRRIQELNE 66 Query: 322 TTLNPVKLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLR 379 L+ + F IMS LA E+ +VA LGP+G+F+++ A K G V Sbjct: 67 GPLSNDTVIRFFREIMSACLALEKPLEVA-------FLGPEGTFTQQAAFKHFGHAVKTV 119 Query: 380 YCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVA 439 +T EI VE+G +G+VP+ENS G + +D LL +++ GE ++ V+ L+ Sbjct: 120 PAATISEIFNAVETGLCQFGVVPVENSTEGVISHTLDRLLASPLKICGEVEIRVHQNLLG 179 Query: 440 KRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSE 497 + L +I T+YSH Q++AQC +++ YLP+ +S ++AAR+ D AAI Sbjct: 180 LAE-NLADITTVYSHQQSLAQCRQWLDKYLPNPQRVAVSSNAEAARLAASDKQFAAIAGI 238 Query: 498 NAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGALKDVLE 556 AA Y+L V+ K I+D+ N TRF +I +++ S GK TSL +KPGAL LE Sbjct: 239 AAADVYQLPVIEKNIEDI-ANNTTRFIIIGQQTSTSTGKDKTSLVVSTGNKPGALHRTLE 297 Query: 557 VFHKKGFNLRKLESRPAGTGLGDYVFFVEVE 587 F + G ++ +ESRP+ GL DYVFF++V+ Sbjct: 298 PFARFGVDMVNIESRPSHQGLWDYVFFIDVQ 328 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: 390 Number of extensions: 18 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: 361 Length adjustment: 33 Effective length of query: 587 Effective length of database: 328 Effective search space: 192536 Effective search space used: 192536 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