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 <-- 0.714 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1bmta2) 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 d1bmta2 Methionine synthase,​ C-​terminal domainCobalamin (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 <-- 0.714 --> Hit
DALI alignment (Z-score: 7.0 Raw score:698.30) d1qyca_ 1 ---GSRSRILLIG----aTGYIGRHVAKASLDLGHPTFLLVRestassnsekaqllesfk 53 :::::::::: :::::::::::::::::::::::: d1bmta2 1 eqgKTNGKMVIATvkgdvHDIGKNIVGVVLQCNNYEIVDLGV------------------ 42 d1qyca_ 54 asganivhgSIDDhaSLVEAVK--NVDVVISTVGSL-QIESQVNIIKAIK-EVGTVkRFF 109 :::: ::::::: :::::::::::: ::::::::::::: ::::: ::: d1bmta2 43 --------mVPAE--KILRTAKevNADLIGLSGLITpSLDEMVNVAKEMErQGFTI-PLL 91 d1qyca_ 110 PSEFgndvdnvhavepaksvfeVKAKVRRAIEAE-GIPYTYVSsncfagyflrslaqagl 168 :::: :::::::::::: :::::::: d1bmta2 92 IGGA----------------ttSKAHTAVKIEQNySGPTVYVQ----------------- 118 d1qyca_ 169 tapprdkvvilgdgnarvvfvkeedIGTFTIKAVDD-------PRTLNKTlylrlpantl 221 ::::::::::: ::::::: d1bmta2 119 -------------------------NASRTVGVVAAllsdtqrDDFVART---------- 143 d1qyca_ 222 slnelvalwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeig 281 d1bmta2 144 ------------------------------------------------------------ 144 d1qyca_ 282 pagveasqlypdvkyttvdeylsnfv 307 d1bmta2 144 -------------rkeyetvriqhgr 156 FAST alignment (Normalized score: 5.68 Raw score:1244.00) d1qyca_ 1 GS-----RSRILLIGAT--------GYIGRHVAKASLDLGHPTFLLVRESTASSNSEKAQ 47 :::::: ::::::::::::::::::::: d1bmta2 1 --EQGKTNGKMVI----ATVKGDVHDIGKNIVGVVLQCNNYEIVDL-------------- 40 d1qyca_ 48 LLESFKASGANIVHGSI---DDHASLVEAVK--NVDVVISTV-GSLQIESQVNIIKAIKE 101 ::::::::::: ::::::::: ::::::::::::::::: d1bmta2 41 -----------------GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMER 83 d1qyca_ 102 VGTV--KRFFPSEFGNDVDNVHAVEPAKS------VFEVK-AKVRRAIEAEGIPYTYVSS 152 :: :::: ::::: :::::: :::::::: d1bmta2 84 QG--FTIPLL-------------------IGGATTSKAHTAVKIEQN---YSGPTVYV-- 117 d1qyca_ 153 NCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEED-IGTFTIKA---VDDPRTL 208 :::::::: ::::::: d1bmta2 118 -----------------------------------------QNASRTVGVVAALLSDTQR 136 d1qyca_ 209 NKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHS 268 d1bmta2 137 ------------------------------------------------------------ 137 d1qyca_ 269 IFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYLSNFV-------------------- 307 d1bmta2 137 ---------------------------------------DDFVARTRKEYETVRIQHGR 156 TMalign alignment (TM-score: 0.36 Raw score:109.81) d1qyca_ 1 ---GSRSRILLIG----ATGYIGRHVAKASLDLGHPTFLLVRESTASSNSEKAQLLESFK 53 :::::::::: ::::::::::::::::::::::::: d1bmta2 1 EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGV------------------ 42 d1qyca_ 54 ASGANIVHGSIDDHASLVEAVK-N-VDVVISTVGS-LQIESQVNIIKAIK-EVGTVKRFF 109 ::: :: ::::::: : :::::::::: :::::::::::::: ::::: ::: d1bmta2 43 --------MVP-AE-KILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTI-PLL 91 d1qyca_ 110 PSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLRSLAQAGLT 169 ::::::::: ::::::::::::::::: : d1bmta2 92 IGGATTSKA---------------HTAVKIEQNYSGPTVYV-Q----------------- 118 d1qyca_ 170 APPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDD------P-RTLN-KTLYLRLPANTL 221 ::::::::::: : :::: :: d1bmta2 119 ------------------------NASRTVGVVAALLSDTQRDDFVARTR---------- 144 d1qyca_ 222 SLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIG 281 d1bmta2 145 ------------------------------------------------------------ 145 d1qyca_ 282 PAG---------VEASQLYPDVKYTTVDEYLSNFV 307 ::: d1bmta2 145 KEYETVRIQHGR----------------------- 156 HHsearch alignment (Probability: 0.36 E-value:0.03) d1qyca_ 92 QVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVEPAKSVFEVKAKVRRAIEAEGIPYTYVS 151 :::::::::::: :::::::::::: ::::::::::::::::::::::: d1bmta2 46 AEKILRTAKEVN-ADLIGLSGLITP------------SLDEMVNVAKEMERQGFTIPLLI 92