This is a simple question that requires a complicated answer. First it depends on the type of sequence you are working on: nucleic acid or protein. Homology is more difficult to define in the case of nucleic acids that with proteins. Therefore one may prefer to work with protein sequences rather that with DNA or RNA in order to decide whether or not two sequences are homologous, paralogous or random. Moreover, the E value is a statistical value that depends both on the length of your query sequence as well as on the size (number of sequences) of your search database. These issues are being described in detail in my chapter "Phylogenetic analysis using protein sequences" which can be downloaded from ResearchGate at the following address:
https://www.researchgate.net/publication/326294021_Phylogenetic_analysis_using_protein_sequences
Hi Sarita Kumari,
>
source: https://dx.doi.org/10.1002%2F0471250953.bi0301s42
Thanks to all distinguished scientist, for answers you mentioned above. my point is that when we all are doing BLAST and based on similarity used the terminology homologous for that query genes. so what should be the similarity percentage for being homologous
Dear Sarita,
To answer your last question, I tend to use the following rules of thumb. I do not work with similarity but with the better defined percentage of identical residues in the overall protein sequence. Moreover, it can only be applied to full length proteins of more than about 100 residues long. If two proteins share about 20% identical residues they are likely to be homologous, thus catalyze a similar catalytic reactions. If they share 50% identity, or more, they are most likely orthologous proteins that catalyze not only similar reactions, but also have the same function within the cell.
A nice example is that of the mitochondrial and cytosolic malate dehydrogenases of human and mouse. The two cytosolic isoenzymes share 96.4% identity and the two mitochondrial isoenzymes share 95% identity, respectively, while the mitochondrial and cytosolic enzymes share only about 19% identity. (see the result below using a Clustal alignment and distance matrix.
CLUSTAL 2.1 multiple sequence alignment
sp|P40926|MDHM_HUMAN MLSALARPASAALRRSFSTSAQNNAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAH
sp|P08249|MDHM_MOUSE MLSALARPAGAALRRSFSTSAQNNAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAH
sp|P40925|MDHC_HUMAN ----MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLME
sp|P14152|MDHC_MOUSE ----MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLME
::.* . : : . * . *: * .**: *:* : . : : : .
sp|P40926|MDHM_HUMAN TPGVAADLSHIETKAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATI
sp|P08249|MDHM_MOUSE TPGVAADLSHIETRANVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATI
sp|P40925|MDHC_HUMAN LQDCALPL--------LKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKI
sp|P14152|MDHC_MOUSE LQDCALPL--------LQDVIATDKEEIAFKDLDVAVLVGSMPRREGMERKDLLKANVKI
. * * ::. :..:: .:*. **.:: ..:**: ** *.**:::*..*
sp|P40926|MDHM_HUMAN VATLTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTF
sp|P08249|MDHM_MOUSE VATLTAACAQHCPEAMVCIIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTF
sp|P40925|MDHC_HUMAN FKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPS--IPKENFSCLTRLDHNRAKAQ
sp|P14152|MDHC_MOUSE FKSQGTALEKYAKKSVKVIVVGNPANTNCLTASKSAPS--IPKENFSCLTRLDHNRAKSQ
. : :* ::. ::: ::.. .* :**. ::: :* ** **::
sp|P40926|MDHM_HUMAN VAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQD-----------QLTALTGR
sp|P08249|MDHM_MOUSE VAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQD-----------QLATLTGR
sp|P40925|MDHC_HUMAN IALKLGVTANDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTT
sp|P14152|MDHC_MOUSE IALKLGVTADDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFITT
:* *: . *: :* *: ..* * :.:.. *:: : :
sp|P40926|MDHM_HUMAN IQEAGTEVVKAKAGAGSATLSMAYAG--ARFVFSLVDAMNGKEGVVECSFVKSQETECTY
sp|P08249|MDHM_MOUSE IQEAGTEVVKAKAGAGSATLSMAYAG--ARFVFSLVDAMNGKEGVVECSFVQSKETECTY
sp|P40925|MDHC_HUMAN VQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYG-VPDDLL
sp|P14152|MDHC_MOUSE VQQRGAAVIKARKLSSAMSAAKAIADHIRDIWFGTPEGEFVSMGVISDGNSYG-VPDDLL
:*: *: *:**: :.: : : * .. : *. :. . **:. . . .:
sp|P40926|MDHM_HUMAN FSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPELKASIKKGEDFVKTLK
sp|P08249|MDHM_MOUSE FSTPLLLGKKGLEKNLGIGKITPFEEKMIAEAIPELKASIKKGEDFVKNMK
sp|P40925|MDHC_HUMAN YSFPVVIKNKTWKFVEGLP-INDFSREKMDLTAKELTEEKESAFEFLSSA-
sp|P14152|MDHC_MOUSE YSFPVVIKNKTWKFVEGLP-INDFSREKMDLTAKELTEEKETAFEFLSSA-
:* *::: :* : *: :. *..: : : **. . :.. :*:..
Distance matrix
4
sp|P40926|MDHM_HUMAN 0.000 0.050 0.819 0.819
sp|P08249|MDHM_MOUSE 0.050 0.000 0.813 0.813
sp|P40925|MDHC_HUMAN 0.819 0.813 0.000 0.036
sp|P14152|MDHC_MOUSE 0.819 0.813 0.036 0.000
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