HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.613 --> Intermediate <-- 1.033 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1g8aa_) through the intermediate protein (d1ps9a3) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ps9a3 2,​4-​dienoyl-​CoA reductase,​ middle domainNucleotide-​binding domainNucleotide-​binding domainα/β
Hit d1g8aa_ Fibrillarin homologueS-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/β

Supporting Alignments

Query <-- 1.613 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 1.033 --> Hit
DALI alignment (Z-score: 5.0 Raw score:473.40) d1ps9a3 1 --------------------------intcigcnqacldqifvgkvtsclVNPR-----a 29 :::: d1g8aa_ 1 mvevkkhkfpgvytvidddgseriatknlvpgqrvygervikwegeeyriWNPNrsklga 60 d1ps9a3 30 chetkmpilpavQKKNLAVVGAGPAglAFAINAAARG---HQVTLFDAHSEIggqfniak 86 ::::::::::::: :::::::::: :::::::::::: d1g8aa_ 61 aimnglknfpikPGKSVLYLGIASG--TTASHVSDIVgweGKIFGIEFSPRV-------- 110 d1ps9a3 87 qipgkeefyetlryYRRMIEVTG-VTLKLnHTVT-ADQL----qAFDETILASGIPNR-A 139 ::::::::: ::::: :::: :::: :::::::::::::: : d1g8aa_ 111 -----------lreLVPIVEERRnIVPIL-GDATkPEEYralvpKVDVIFEDVAQPTQaK 158 d1ps9a3 140 LAQPLIDS----gKTVHLIggcDVAM---------------------------------- 161 :::::::: :::::: :::: d1g8aa_ 159 ILIDNAEVylkrgGYGMIA---VKSRsidvtkepeqvfreverelseyfevierlnlepy 215 d1ps9a3 162 -ELDArraiaqgtrlalei 179 :::: d1g8aa_ 216 eKDHA-------lfvvrkt 227 FAST alignment (Normalized score: 3.77 Raw score:760.30) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHET----------------------KMPIL 38 ::::: d1g8aa_ 1 ---------------------------------MVEVKKHKFPGVYTVIDDDGSERIATK 27 d1ps9a3 39 PA--------------------------------------------VQKKNLAVVGAGPA 54 :::::::::: d1g8aa_ 28 --NLVPGQRVYGERVIKWEGEEYRIWNPNRSKLGAAIMNGLKNFPIKPGKSVLYLG---- 81 d1ps9a3 55 --GLAFAINAAA---RGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYET--LRYYRRMIEV 107 :::::::::: :::::::::::: :::::::::: d1g8aa_ 82 IASGTTASHVSDIVGWEGKIFGIEFSP---------------------RVLRELVPIVEE 120 d1ps9a3 108 T-GVTLKLNHT-VTADQL-----QAFDETILASGIP-NRALAQPLID----SGKTVHLIG 155 : :::: :::: ::::: ::::::::::::: :::::::::: :::::::: d1g8aa_ 121 RRNIVP-ILGDATKPEE-YRALVPKVDVIFEDVAQPTQAKILIDNAEVYLKRGGYGMIA- 177 d1ps9a3 156 GCDVAMELDARRAIAQGTRLALEI------------------------------------ 179 d1g8aa_ 178 ------------------------VKSRSIDVTKEPEQVFREVERELSEYFEVIERLNLE 213 d1ps9a3 180 -------------- 180 d1g8aa_ 214 PYEKDHALFVVRKT 227 TMalign alignment (TM-score: 0.48 Raw score:85.74) d1ps9a3 1 --------------INTCIGCNQACLDQIFVGKVTSCLVNPR---ACHETKMPIL-P--- 39 : ::::::::: : d1g8aa_ 1 MVEVKKHKFPGVYT---------------------------VIDD-DGSERIATKNLVPG 32 d1ps9a3 40 --------------------------------------AVQKKNLAVVGAGPAGLAFAIN 61 ::::::::::::::: ::::: d1g8aa_ 33 QRVYGERVIKWEGEEYRIWNPNRSKLGAAIMNGLKNFPIKPGKSVLYLGIASG--TTASH 90 d1ps9a3 62 AAAR-G--HQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTG-VTLKLNHT 117 :::: : ::::::::::::: :: ::::::::: ::::: :: d1g8aa_ 91 VSDIVGWEGKIFGIEFSPRVL------------------RE-LVPIVEERRNIVPIL-GD 130 d1ps9a3 118 V-TADQ-L---QAFDETILASGIPNR-ALAQPLID--S-G-KTVHLIGGCDVAME----- 162 : :::: : ::::::::::::::: :::::::: : : :::::: ::::: d1g8aa_ 131 ATKPEEYRALVPKVDVIFEDVAQPTQAKILIDNAEVYLKRGGYGMIA---VKSRSIDVTK 187 d1ps9a3 163 ------------------------L--DARRA--IAQG-TRL----ALEI 179 : ::: :: : d1g8aa_ 188 EPEQVFREVERELSEYFEVIERLNLEP--YEKDH--ALF--VVRKT---- 227 HHsearch alignment (Probability: 0.21 E-value:0.01) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINA-AARGHQVTLFDAHSEI 78 :::::::::::::::::::::::::: :::::::::::::::: d1g8aa_ 68 NFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIFGIEFSPRV 110