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 <-- 0.813 --> Intermediate <-- 0.993 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ccwa_) through the intermediate protein (d1qyca_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1qyca_ Phenylcoumaran benzylic ether reductaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1ccwa_ Glutamate mutase,​ small subunitCobalamin (vitamin B12)-​binding domainFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 0.813 --> Intermediate
DALI alignment (Z-score: 4.9 Raw score:359.30) query 1 gMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAfwglllLRDPekasqedks 60 :::::::::: ::::::::::::::::::::::: :::: d1qyca_ 1 -GSRSRILLIG-----atGYIGRHVAKASLDLGHPTFLLVR-----eSTAS--------- 40 query 61 lyeqafssltpREAEelplskmnlggigkkmllemmkeekapkLSDLLSGARKKEVKFY- 119 :::: :::::::::::::::: d1qyca_ 41 -----------SNSE----------------------------KAQLLESFKASGANIVh 61 query 120 AXQLsveimgfkkeelfpevqimDVKEYLKNALESDLQLFI------------------- 160 :::: :::::::::::::::::: d1qyca_ 62 GSID-------------------DHASLVEAVKNVDVVISTvgslqiesqvniikaikev 102 query 161 ------------------------------------------------------------ 161 d1qyca_ 103 gtvkrffpsefgndvdnvhavepaksvfevkakvrraieaegipytyvssncfagyflrs 162 query 161 ------------------------------------------------------------ 161 d1qyca_ 163 laqagltapprdkvvilgdgnarvvfvkeedigtftikavddprtlnktlylrlpantls 222 query 161 ------------------------------------------------------------ 161 d1qyca_ 223 lnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeigp 282 query 161 ------------------------- 161 d1qyca_ 283 agveasqlypdvkyttvdeylsnfv 307 FAST alignment (Normalized score: 3.09 Raw score:685.40) query 1 GMENKKMNLLLFSGDYDK----ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQ 56 :::::::: ::::::::::::::::::::::: d1qyca_ 1 -GSRSRILL---------IGATGYIGRHVAKASLDLGHPTFLLVR--------------- 35 query 57 EDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP--------KLSDLL 108 :::::: d1qyca_ 36 ----------------------------------------------ESTASSNSEKAQLL 49 query 109 SGARKKEVKFYAXQLSVEIMGFKKEELFPEVQI----MDVKEYLKNALESDLQLFI---- 160 ::::::::::: ::::::::::::::::: d1qyca_ 50 ESFKASGANIV----------------------HGSIDDHASLVEAVKNVDVVI--STVG 85 query 161 ------------------------------------------------------------ 161 d1qyca_ 86 SLQIESQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGI 145 query 161 ------------------------------------------------------------ 161 d1qyca_ 146 PYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDP 205 query 161 ------------------------------------------------------------ 161 d1qyca_ 206 RTLNKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAI 265 query 161 ------------------------------------------ 161 d1qyca_ 266 SHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV 307 TMalign alignment (TM-score: 0.36 Raw score:58.19) query 1 GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKS 60 :: ::::::::::::::::::::::::: : ::::::: :: d1qyca_ 1 GS--RSRILLIGATGYIGRHVAKASLDLG----H-PTFLLVR--ES-------------- 37 query 61 LYEQAFSSLTPR-EAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFY 119 ::::::: ::: : :: ::::: :::: d1qyca_ 38 -----TASSNSEKAQL-L--------------------------ES-FKASG----ANIV 60 query 120 AXQLSVE-IMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI------------------ 160 ::::: : :::::::::: : ::::: d1qyca_ 61 HGSID-DH---------------ASLVEAVKNV--D-VVISTVGSLQIESQVNIIKAIKE 101 query 161 ------------------------------------------------------------ 161 d1qyca_ 102 VGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLR 161 query 161 ------------------------------------------------------------ 161 d1qyca_ 162 SLAQAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDPRTLNKTLYLRLPANTL 221 query 161 ------------------------------------------------------------ 161 d1qyca_ 222 SLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIG 281 query 161 -------------------------- 161 d1qyca_ 282 PAGVEASQLYPDVKYTTVDEYLSNFV 307 HHsearch alignment (Probability: 0.02 E-value:0.33) query 89 KKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::: d1qyca_ 245 EEEVLKLIADTPF-PANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYL 303 query 149 KN 150 :: d1qyca_ 304 SN 305
Intermediate <-- 0.993 --> Hit
DALI alignment (Z-score: 6.6 Raw score:649.40) d1qyca_ 1 GSRSRILLIG----aTGYIGRHVAKASLDLGHPTFLLVrestassnsekaqllesfkasg 56 :::::::::: ::::::::::::::::::::::: d1ccwa_ 1 MEKKTIVLGVigsdcHAVGNKILDHAFTNAGFNVVNIG---------------------- 38 d1qyca_ 57 anivhGSIDdhaSLVEAVK--NVDVVISTVGSLQIE-SQVNIIKAIKE--VGTVkRFFPS 111 :::: ::::::: ::::::::::::::: ::::::::::: :::: ::::: d1ccwa_ 39 ---vlSPQE---LFIKAAIetKADAILVSSLYGQGEiDCKGLRQKCDEagLEGI-LLYVG 91 d1qyca_ 112 EfgndvdnvhavepAKSVFEVKAKVRRAIeaegipYTYVSSncfagyflrslaqagltap 171 : ::::::::::::::: :::::: d1ccwa_ 92 G--------nivvgKQHWPDVEKRFKDMG-----yDRVYAP------------------- 119 d1qyca_ 172 prdkvvilgdgnarvvfvkeedIGTFTIKAVDDPrtlnktlylrlpantlslnelvalwe 231 :::::::::::: d1ccwa_ 120 --------------------gtPPEVGIADLKKD-------------------------- 133 d1qyca_ 232 kkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeigpagveasqly 291 d1ccwa_ 134 ------------------------------------------------------------ 134 d1qyca_ 292 pdvkyttvdeylsnfv 307 d1ccwa_ 134 ------------lnie 137 FAST alignment (Normalized score: 5.38 Raw score:1103.00) d1qyca_ 1 GSRSRILLIGAT--------GYIGRHVAKASLDLGHPTFLLVRESTASSNSEKAQLLESF 52 :::::::: ::::::::::::::::::::: d1ccwa_ 1 MEKKTIVL----GVIGSDCHAVGNKILDHAFTNAGFNVVNI------------------- 37 d1qyca_ 53 KASGANIVHGSI---DDHASLVEAVK--NVDVVISTVGSLQI-ESQVNIIKAIKE--VGT 104 ::::::::::: :::::::::::::: :::::::::::: ::: d1ccwa_ 38 ------------GVLSPQELFIKAAIETKADAILVSSLYGQGEIDCKGLRQKCDEAGLEG 85 d1qyca_ 105 VKRFFPSEFGNDVDNVHAVEPAK---------SVFEVKAKVRRAIEAEGIP---YTYVSS 152 ::::: ::::::::::: :::: d1ccwa_ 86 -ILLYV-----------------GGNIVVGKQHWPDVEKRFKD--------MGYDRVY-- 117 d1qyca_ 153 NCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEED----IGTFTIKAVDDPRTL 208 :::::::::: d1ccwa_ 118 -----------------------------------------APGTPPEVGIADLK----- 131 d1qyca_ 209 NKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHS 268 d1ccwa_ 132 ------------------------------------------------------------ 132 d1qyca_ 269 IFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV------ 307 d1ccwa_ 132 ---------------------------------------KDLNIE 137 TMalign alignment (TM-score: 0.34 Raw score:104.14) d1qyca_ 1 GSRSRILLIG-----ATGYIGRHVAKASLDLGHPTFLLVRESTASSNSEKAQLLESFKAS 55 :::::::::: :::: :::::::::::::::::::: d1ccwa_ 1 MEKKTIVLGVIGSDCHAVG-NKILDHAFTNAGFNVVNIGV-------------------- 39 d1qyca_ 56 GANIVHGSIDDHASLVEAVK-N-VDVVISTVGSLQIE-SQVNIIKAIKE-VGTVKRFFPS 111 :::: : ::::::: : :::::::::::::: ::::::::::: :::::::::: d1ccwa_ 40 ------LSPQ-E-LFIKAAIETKADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLYVG 91 d1qyca_ 112 EFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLRSLAQAGLTAP 171 ::: : ::::::::::::::::: : ::::: : : d1ccwa_ 92 GNI--V------VGKQHWPDVEKRFKDMG----Y-DRVYA-P-G---------------- 120 d1qyca_ 172 PRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDPRTL-NKTLYLRLPANTLSLNELVALW 230 : :::::::::::: :: d1ccwa_ 121 -------------------T--PPEVGIADLKKD-LNI---------------------- 136 d1qyca_ 231 EKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQL 290 d1ccwa_ 137 ------------------------------------------------------------ 137 d1qyca_ 291 YPDVKYTTVDEYLSNFV 307 : d1ccwa_ 137 E---------------- 137 HHsearch alignment (Probability: 0.22 E-value:0.10) d1qyca_ 15 IGRH-VAKASLDLGHPTFLLVR 35 :::: ::::::::::::::::: d1ccwa_ 18 VGNKILDHAFTNAGFNVVNIGV 39