Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate Echvi_0123 Echvi_0123 Prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__Cola:Echvi_0123 Length = 279 Score = 137 bits (346), Expect = 3e-37 Identities = 86/281 (30%), Positives = 139/281 (49%), Gaps = 16/281 (5%) Query: 101 PHSARIAFLGPKGSYSHLAARQYAARHFEQFIES-GCAKFADIFNQVETGQADYAVVPIE 159 PH ++A G KGSY + Q A F Q I C F+D+ + + AD V+ +E Sbjct: 5 PHQQKVAIQGIKGSYHY----QVALNQFGQDIHVIECLTFSDLVKSITSNDADIGVLALE 60 Query: 160 NTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKF 219 N+ +GAI YDL+ +L ++GE L I H L+V + I V SHP QC F Sbjct: 61 NSIAGAILPNYDLMDRNNLQVIGEFYLPISHQLMVLKGQSIDDITEVRSHPMALLQCKAF 120 Query: 220 LNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTR 279 +YP K+ T++ +++++ V A+ ++ YGL +L + N TR Sbjct: 121 FEQYPQIKLIEDLDTASVAKEISEQHLQGVGAIAGKSAAEFYGLDILASDIQTIKNNITR 180 Query: 280 FVVLARKAINVSDQVPA----KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHG 335 F ++ N +D P K ++ + + G+L + L + + L +T+++S P+ Sbjct: 181 FCIVK----NAADAKPVIGFDKASIKVTIKNEQGSLAKVLTTMSAYRLDLTKIQSLPVID 236 Query: 336 NPWEEMFYLDIQ-ANLESAEMQKALKELGEITRSMKVLGCY 375 PW F++D+ NLE + Q+ALKEL +KVLG Y Sbjct: 237 QPWHYAFFIDLLFENLE--DYQQALKELKANGHQIKVLGEY 275 Lambda K H 0.318 0.132 0.374 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: 210 Number of extensions: 12 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: 386 Length of database: 279 Length adjustment: 28 Effective length of query: 358 Effective length of database: 251 Effective search space: 89858 Effective search space used: 89858 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 (21.8 bits) S2: 49 (23.5 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