PhyloBlocks -- http://compbio.mcs.anl.gov/ulrich/phyloblock/
SWMMER -- http://compbio.mcs.anl.gov/svmmer/
BlockBlast --
http://compbio.mcs.anl.gov/blast/psiblast_phylo.html
PhyloBlocks Phyloblocks and SVMMER -- description
Motivation:
The current rsolution of such tools as: InterPro,
Pfam, (COGs, Hobagen, etc. are unable to discriminate closely related,
homolgous sequences as shown by WIT3
knowledge base ( example
IPB001917)
PhyloBlocks allows us to develop a library of BLOCK HMM profiles corresponding
to particular enzymatic functions or evolutionary versions of enzymes.
Applications:
PhyloBlocks - (1) Identification, classification and characterization
of proteins utilizing refined BLOCKS. (2) Phylogeneic analysis using BLOCKs
distribution to identify cases of convergent/divergent evolution of enzymes.
SVMmer - (1) Automated classification and prediction of protein function.
(2) Identification of conserved amino acid residues responsible for the
functionality of a proteins sequence.
Input to PhyloBlocks from:
| Input from | Input | Example | Precomputed
results |
| BlockBlast | Sequence in FASTA
format |
>gi|14521874|ref|NP_127350.1|
5-AMINOLEVULINIC ACID SYNTHASE [Pyrococcus abyssi]
MVLMGKLDWIKEELEELKKKGLYVTIRVLQSAQGPWVVVNGKRVLNMCSNNYLGLAAHPKIKEAAIRAIL DYGVGAGAVRTIAGTMELHVELEEKLAKFKKREAAILFQSGYNANLGAISALLRKGEDGIFLSEELNHAS IIDGMRLSGAPKVIYKHLDMDDLKKKLEENKDKKKKIIVTDGVFSMDGDLAPLPEIVELAEQYDAIVYVD DAHGEGVLGSHGRGIVDHFNLHDKVDFEMGTLSKAFGVIGGYVAGPEEAIEYLKQRARPFLFSSAMNPPD VAAAIAAVEILQKSDDLVKKLWDNTHFLQKGLRDLGYDLGNTKHPITPVMLYDEKLAQEFSRRLYEEYNI FAQAIVYPTVPLGTARIRLEPSAAHTKEDLKLVIDAFEDLGKKTGFLK |
BlockBlast
From this page you can select sequences and submit it to PhyloBlocks |
| From COGs | Select an
input from COGs option and input a COG ID |
COG0156 | |
| From SubUnits database | subunit info | EC 2.7.1.11 | |
| From Hobagen | |||
| From EC | 5-aminolevulinic acid synthase (EC 2.3.1.37) | ||
| From WIT3 KnowledgeBase | Start from the WIT3 Family | ||
