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 <-- 1.567 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1vbfa_) 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 d1vbfa_ Protein-​L-​isoaspartyl O-​methyltransferaseS-​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 <-- 1.567 --> Hit
DALI alignment (Z-score: 4.0 Raw score:423.50) d1ps9a3 1 -----------------------------inTCIGC-NQACldqifvgkvtSCLV----- 25 ::::: :::: :::: d1vbfa_ 1 asekeeilrkiktqelaeafnkvdrslflpeNLKDYaYAHT----------HEALpilpg 50 d1ps9a3 26 ---nprachetkmpilpaVQKKNLAVVGAGPagLAFAINAAARGHQVTLFDAHSEIggqf 82 ::::::::::::: ::::::::::::::::::::::: d1vbfa_ 51 inttalnlgifmldeldlHKGQKVLEIGTGI--GYYTALIAEIVDKVVSVEINEKM---- 104 d1ps9a3 83 niakqipgkeefyetlryYRRMIEVTG-VTLKLnHTVTA--DQLQAFDETILAsGIPNRA 139 ::::::::: ::::: ::::: :::::::::::: :::::: d1vbfa_ 105 ---------------ynyASKLLSYYNnIKLIL-GDGTLgyEEEKPYDRVVVW-ATAPTL 147 d1ps9a3 140 lAQPLID---sGKTVHLiggCDVA---------------------MELD----------- 164 :::::: :::::: :::: :::: d1vbfa_ 148 -LCKPYEqlkeGGIMIL---PIGVgrvqklykvikkgnspslenlGEVMfgrigglygfy 203 d1ps9a3 165 ------arraiaqgtrlalei 179 d1vbfa_ 204 ddyddiefrvnklerqiksil 224 FAST alignment (Normalized score: 3.77 Raw score:755.90) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPR----ACHETKMPILP----------------- 39 ::::::::: d1vbfa_ 1 ----------------------------ASEKEEILRKIKT--QELAEAFNKVDRSLFLP 30 d1ps9a3 40 -------------------------------------AVQKKNLAVVGAGPAG-LAFAIN 61 ::::::::::::: :::::: d1vbfa_ 31 ENLKDYAYAHTHEALPILPGINTTALNLGIFMLDELDLHKGQKVLEIGTG---IGYYTAL 87 d1ps9a3 62 AAARG--HQVTLFDAHSEIGGQFNIAKQIPGKEEF-YETLRYYRRMIEVT-GVTLKLNHT 117 ::: :::::::: :::::::::::::: ::::: ::: d1vbfa_ 88 IAE--IVDKVVSVEI--------------------NEKMYNYASKLLSYYNNIKLI-LGD 124 d1ps9a3 118 VT---ADQLQAFDETILASGIPNRAL-------AQPLID---SGKTVHLIGG--CDVAME 162 : :::::::::::: :::::: ::::: :::: d1vbfa_ 125 G-TLGYEEEKPYDRVVV---------WATAPTLLCKPYEQLKEGGIM-----ILPIGV-- 167 d1ps9a3 163 LDARRAIAQGTRLALEI------------------------------------------- 179 d1vbfa_ 168 -----------------GRVQKLYKVIKKGNSPSLENLGEVMFGRIGGLYGFYDDYDDIE 210 d1ps9a3 180 -------------- 180 d1vbfa_ 211 FRVNKLERQIKSIL 224 TMalign alignment (TM-score: 0.46 Raw score:82.83) d1ps9a3 1 -------------------------IN--TCIGCNQ-ACLDQIFVGKVTSCL-------V 25 :: ::::::: :: : ::::: : d1vbfa_ 1 ASEKEEILRKIKTQELAEAFNKVDRSLFLPENLKDYAYA--H-----THEALPILPGINT 53 d1ps9a3 26 -NPR----------ACHETKMPILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDA 74 ::: :::::::::::::: ::::::::::::::::::: d1vbfa_ 54 TALNLGIFMLDELD-----------LHKGQKVLEIGTGI--GYYTALIAEIVDKVVSVEI 100 d1ps9a3 75 HSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTG-VTLKLNHTVTADQL-QAFDETILA 132 ::::: :: ::::::::: :::::::::::::: ::::::::: d1vbfa_ 101 NEKMY------------------NY-ASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVW 141 d1ps9a3 133 SGIPNRALAQP-LIDS-G-KTVHLI------GGCD-----------------VAMELD-- 164 : :::::::: :::: : :::::: ::: :: :: d1vbfa_ 142 -A-TAPTLLCKPYEQLKEGGIMILPIGVGRV-QKLYKVIKKGNSPSLENLGEVM--FGRI 196 d1ps9a3 165 ----------------------------ARRAIAQGTRLALEI 179 d1vbfa_ 197 GGLYGFYDDYDDIEFRVNKLERQIKSIL--------------- 224 HHsearch alignment (Probability: 0.92 E-value:0.00) d1ps9a3 37 ILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYE 96 ::::::::::::::::: ::::: :::::::::::::::::: d1vbfa_ 65 ELDLHKGQKVLEIGTGI-GYYTA-LIAEIVDKVVSVEINEKM------------------ 104 d1ps9a3 97 TLRYYRRM-IEVTGVTLKLNHTV-TADQLQAFDETILASGIPNRALAQ--PLIDSGKTVH 152 ::::::: :::::::::::::: :::::::::::::::::::::::: :::::::::: d1vbfa_ 105 -YNYASKLLSYYNNIKLILGDGTLGYEEEKPYDRVVVWATAPTLLCKPYEQLKEGGIMIL 163 d1ps9a3 153 LIGGCD 158 :::::: d1vbfa_ 164 PIGVGR 169