Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate WP_011841614.1 RSPH17029_RS11915 prephenate dehydratase
Query= BRENDA::Q5NLV8 (337 letters) >NCBI__GCF_000015985.1:WP_011841614.1 Length = 277 Score = 221 bits (564), Expect = 1e-62 Identities = 124/277 (44%), Positives = 172/277 (62%), Gaps = 11/277 (3%) Query: 57 TKAVAFQGAPGCNSNIAIQDLFPDSLPLPCFSFADALTAVKEGRAGRAMIPIENSLNGRV 116 T +AFQG PG S+ A + P+ +PC +F D + V+ G A AM+P+ENS GRV Sbjct: 2 TGRIAFQGEPGAYSHQACRQARPEMEAIPCRTFEDVIELVRAGEADLAMLPVENSTYGRV 61 Query: 117 ADMHFLLPESGLTIQAEYFLPINHCLVAPKGAG--EITHVLSHPQALGQCRHWLQAHNLR 174 AD+H LLP SGL I E F+ ++ L+ +G ++ +SH LGQCR +L+ H++R Sbjct: 62 ADIHTLLPGSGLRIVDESFVRVHINLLTLRGTPIEQVERAMSHTVLLGQCRTFLRGHDIR 121 Query: 175 ALAHADTAGAAAEVADRKQAGLAALSPALAAKLYGLEILEKGIADGDTNITRFVVLA-EA 233 + ADTAG+A VA++ LAAL+ LA ++YGL+++ + I D N TRF+V+A EA Sbjct: 122 PVTGADTAGSARLVAEQGDPALAALASELAGEIYGLDVVARHIEDQSNNTTRFLVMAREA 181 Query: 234 DTALQDLPPIRQNLSGKMMTSLLFTVKNTPSALLNAIKGFGDNQVNMTKLESYQHGASFS 293 D + GKM+T+ F V+N P+AL A+ GF N +NMTKLESY G SF+ Sbjct: 182 DWTRRG--------PGKMVTTFTFRVRNIPAALYKALGGFATNGINMTKLESYMVGGSFT 233 Query: 294 ATQFYADVEGEPSEDNVARALDILQENACDLRILGVY 330 AT+FYAD+EG P + NVA ALD L+ ILGVY Sbjct: 234 ATEFYADIEGHPEDGNVALALDELRFFTSQSEILGVY 270 Lambda K H 0.318 0.132 0.382 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: 217 Number of extensions: 9 Number of successful extensions: 3 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: 337 Length of database: 277 Length adjustment: 27 Effective length of query: 310 Effective length of database: 250 Effective search space: 77500 Effective search space used: 77500 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: 48 (23.1 bits)
This GapMind analysis is from Apr 16 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