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Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html

Citations (SAM, SAM-T99, HMMs)

Sequence numbers correspond to the following labels:

    • T0323 XB5566A, Bacillus halodurans, 221 res
    • gi|34811270|pdb|1P59|A_10:192 Chain A, Structure Of A Non-Covalent Endonuclease Iii-Dna Complex [Taxonomy]
    • gi|34811456|pdb|1ORP|A_10:192 Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate: Estranged-Adenine Complex [Taxonomy]
    • gi|34811453|pdb|1ORN|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate: Estranged-Guanine Complex [Taxonomy]
    • gi|27065214|pdb|1KG6|A_10:169 Chain A, Crystal Structure Of The K142r Mutant Of E.Coli Muty (Core Fragment) [Taxonomy]
    • gi|27065207|pdb|1KG3|A_10:169 Chain A, Crystal Structure Of The Core Fragment Of Muty From E.Coli At 1.55a Resolution [Taxonomy]
    • gi|27065206|pdb|1KG2|A Chain A, Crystal Structure Of The Core Fragment Of Muty From E.Coli At 1.2a Resolution [Taxonomy]
    • gi|5822134|pdb|1MUY|A Chain A, Catalytic Domain Of Muty From Escherichia Coli [Taxonomy]
    • gi|20664167|pdb|1KQJ|A_10:169 Chain A, Crystal Structure Of A Mutant Of Muty Catalytic Domain [Taxonomy]
    • gi|27065210|pdb|1KG5|A_10:169 Chain A, Crystal Structure Of The K142q Mutant Of E.Coli Muty (Core Fragment) [Taxonomy]
    • gi|55670672|pdb|1WEI|A_10:169 Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant Complexed To Adenine [Taxonomy]
    • gi|55670670|pdb|1WEF|A Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant [Taxonomy]
    • gi|14278394|pdb|1FN7|A_91:311 Chain A, Coupling Of Damage Recognition And Catalysis By A Human Base-Excision Dna Repair Protein [Taxonomy]
    • gi|28948369|pdb|1HU0|A_96:316 Chain A, Crystal Structure Of An Hogg1-Dna Borohydride Trapped Intermediate Complex [Taxonomy]
    • gi|28948504|pdb|1LWY|A Chain A, Hogg1 Borohydride-Trapped Intermediate Without 8-Oxoguanine [Taxonomy]
    • gi|28948501|pdb|1LWW|A Chain A, Borohydride-Trapped Hogg1 Intermediate Structure Co- Crystallized With 8-Bromoguanine [Taxonomy]
    • gi|28948498|pdb|1LWV|A Chain A, Borohydride-Trapped Hogg1 Intermediate Structure Co- Crystallized With 8-Aminoguanine [Taxonomy]
    • gi|27065216|pdb|1KG7|A_10:169 Chain A, Crystal Structure Of The E161a Mutant Of E.Coli Muty (Core Fragment) [Taxonomy]
    • gi|55670671|pdb|1WEG|A_10:169 Chain A, Catalytic Domain Od Muty Form Escherichia Coli K142a Mutant [Taxonomy]
    • gi|27065209|pdb|1KG4|A Chain A, Crystal Structure Of The K142a Mutant Of E. Coli Muty (Core Fragment) [Taxonomy]
    • gi|6137464|pdb|1MUD|A_10:169 Chain A, Catalytic Domain Of Muty From Escherichia Coli, D138n Mutant Complexed To Adenine [Taxonomy]
    • gi|5822133|pdb|1MUN| Catalytic Domain Of Muty From Escherichia Coli D138n Mutant [Taxonomy]
    • gi|7546476|pdb|1EBM|A_91:311 Chain A, Crystal Structure Of The Human 8-Oxoguanine Glycosylase (Hogg1) Bound To A Substrate Oligonucleotide [Taxonomy]
    • gi|62738729|pdb|1YQK|A_91:311 Chain A, Human 8-Oxoguanine Glycosylase Crosslinked With Guanine Containing Dna [Taxonomy]
    • gi|28948721|pdb|1N3C|A_91:311 Chain A, Structural And Biochemical Exploration Of A Critical Amino Acid In Human 8-Oxoguanine Glycosylase [Taxonomy]
    • gi|46014904|pdb|1M3Q|A_91:311 Chain A, Crystal Structure Of Hogg1 D268e Mutant With Base-Excised Dna And 8-Aminoguanine [Taxonomy]
    • gi|48425055|pdb|1M3H|A Chain A, Crystal Structure Of Hogg1 D268e Mutant With Product Oligonucleotide [Taxonomy]
    • gi|28948715|pdb|1N39|A Chain A, Structural And Biochemical Exploration Of A Critical Amino Acid In Human 8-Oxoguanine Glycosylase [Taxonomy]
    • gi|28948718|pdb|1N3A|A_91:311 Chain A, Structural And Biochemical Exploration Of A Critical Amino Acid In Human 8-Oxoguanine Glycosylase [Taxonomy]
    • gi|62738738|pdb|1YQR|A_91:311 Chain A, Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked To Oxog Containing Dna [Taxonomy]
    • gi|62738735|pdb|1YQM|A Chain A, Catalytically Inactive Human 8-Oxoguanine Glycosylase Crosslinked To 7-Deazaguanine Containing Dna [Taxonomy]
    • gi|62738732|pdb|1YQL|A Chain A, Catalytically Inactive Hogg1 Crosslinked With 7-Deaza-8- Azaguanine Containing Dna [Taxonomy]
    • gi|46015544|pdb|1RRQ|A_16:201 Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An A:oxog Pair [Taxonomy]
    • gi|62738158|pdb|1VRL|A_16:201 Chain A, Muty Adenine Glycosylase In Complex With Dna And Soaked Adenine Free Base [Taxonomy]
    • gi|46015550|pdb|1RRT|A Chain A, Muty Adenine Glycosylase In Complex With Dna And Soaked Adenine Free Base [Taxonomy]
    • gi|46015547|pdb|1RRS|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An Abasic Site [Taxonomy]
    • gi|73977978|ref|XP_539632.2|_104:288 PREDICTED: similar to A/G-specific adenine DNA glycosylase (MutY homolog) (hMYH) [Canis familiaris]
    • gi|48596285|emb|CAA17996.2|_1:198 PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) (DEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) [Mycobacterium tuberculosis H37Rv]
    • gi|31620441|emb|CAD95884.1| PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) (DEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) [Mycobacterium bovis AF2122/97]
    • gi|31794844|ref|NP_857337.1| PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) (DEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) [Mycobacterium bovis AF2122/97]
    • gi|57117142|ref|NP_218191.2| PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) (DEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) [Mycobacterium tuberculosis H37Rv]
    • gi|54037049|sp|P63541|END3_MYCBO Endonuclease III (DNA-(apurinic or apyrimidinic site) lyase) [Taxonomy]
    • gi|54040808|sp|P63540|END3_MYCTU Endonuclease III (DNA-(apurinic or apyrimidinic site) lyase) [Taxonomy]
    • gi|76614310|ref|XP_590672.2|_47:231 PREDICTED: similar to A/G-specific adenine DNA glycosylase (MutY homolog) (hMYH) [Bos taurus]
    • gi|6850320|gb|AAF29397.1|_138:363 Contains similarity to an endonuclease III homolog from Homo sapiens gb|U81285, and contains an Endonuclease III PF|00730 domain. [Arabidopsis thaliana]
    • gi|67599592|ref|XP_666298.1|_1:203 methylated-dna--protein-cysteine methyltransferase (6-o-methylguanine-dna methyltransferase) (o-6-methylguanine-dna-alkyltransferase) [Cryptosporidium hominis TU502]
    • gi|54657267|gb|EAL36069.1| methylated-dna--protein-cysteine methyltransferase (6-o-methylguanine-dna methyltransferase) (o-6-methylguanine-dna-alkyltransferase) [Cryptosporidium hominis]
    • gi|31618100|emb|CAD94211.1|_199:414 PUTATIVE ADA REGULATORY PROTEIN ALKAb [SECOND PART] (Regulatory protein of adaptative response) : Methylated-DNA--protein-cysteine methyltransferase (O-6-methylguanine-DNA alkyltransferase) [Mycobacterium bovis AF2122/97]
    • gi|31792511|ref|NP_855004.1| PUTATIVE ADA REGULATORY PROTEIN ALKAb [SECOND PART] (Regulatory protein of adaptative response) : Methylated-DNA--protein-cysteine methyltransferase (O-6-methylguanine-DNA alkyltransferase) [Mycobacterium bovis AF2122/97]
    • gi|14089508|emb|CAC13268.1|_1:210 METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE (6-O-METHYLGUANINE-DNA METHYLTRANSFERASE) (O-6-METHYLGUANINE-DNA-ALKYLTRANSFERASE) [Mycoplasma pulmonis]
    • gi|15828566|ref|NP_325926.1| METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE (6-O-METHYLGUANINE-DNA METHYLTRANSFERASE) (O-6-METHYLGUANINE-DNA-ALKYLTRANSFERASE) [Mycoplasma pulmonis UAB CTIP]