Align Prephenate dehydratase; PDT; EC 4.2.1.51 (uncharacterized)
to candidate WP_041456041.1 AVA_RS06500 prephenate dehydratase
Query= curated2:P43909 (279 letters) >NCBI__GCF_000204075.1:WP_041456041.1 Length = 290 Score = 172 bits (436), Expect = 8e-48 Identities = 102/290 (35%), Positives = 170/290 (58%), Gaps = 15/290 (5%) Query: 1 MKIAYLGPRGSFCSV--------VAEAAFKSEELYSYATILDVIEAYNEGECDFALVPIE 52 + +A+LGP G++ ++ ++ L Y++I ++A +GE A+VP+E Sbjct: 3 LSVAHLGPPGTYAEQATIFYVKWLSHSSGLEASLRPYSSIAQSLQALAQGETQLAVVPVE 62 Query: 53 NSTEGTVNMSIDKIFHDSNAKVVAEFVLPISQNLLAVSKE-QKIEHIYSHPQALAQTRVY 111 NS EG+V M++D ++ + ++ + +LPI+ L++ + I+ +YSHPQALAQ + + Sbjct: 63 NSIEGSVTMTMDTMWQLDSLQIQSALILPIAHALISCADSLDGIKTVYSHPQALAQCQGW 122 Query: 112 LRKFYPQAQVEITESTSAAAEFVKNNPDLPAAAVANSFAAKMYDLEFIAENIQDLAGNST 171 LR F P Q+ + ST+ A E K DL A+A+S AA++Y+L +A I D A N T Sbjct: 123 LRAFLPNVQLIPSNSTTEALE--KLEYDLSIGAIASSRAAELYNLPILASRINDYAENCT 180 Query: 172 RFWLLGKEKQSFDLNQTKDKVT---LALTLPDNLPGALHKAISVFAWRDIDMTKIESRPL 228 RFW++ + + K+T +A ++P N+PGAL K + VFA DI++++IESRP Sbjct: 181 RFWVISQAESDITHQLPLQKLTHTSIAFSVPANVPGALLKTLQVFAHLDINLSRIESRPT 240 Query: 229 RTRLGQYFFIIDLENNATNSLKIPYALEELAGLGVNVRLLGNYSVYSLGE 278 + LG+Y F IDLE + N+ ++ AL EL +++ G+YSV S + Sbjct: 241 KRSLGEYLFFIDLEAD-VNTPQMKSALLELTTYTEVLKIFGSYSVLSAND 289 Lambda K H 0.317 0.133 0.373 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: 198 Number of extensions: 15 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: 279 Length of database: 290 Length adjustment: 26 Effective length of query: 253 Effective length of database: 264 Effective search space: 66792 Effective search space used: 66792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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