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 <-- 0.627 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1kica_) 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 d1kica_ Inosine-​adenosine-​guanosine preferring nucleoside hydrolaseNucleoside hydrolaseNucleoside hydrolaseα/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 <-- 0.627 --> Hit
DALI alignment (Z-score: 6.9 Raw score:925.10) d1qyca_ 1 gSRSRILLIGATGYIGRHVAKASLDLG--HPTFLLVrestassnSEKAQL-LESFKAS-- 55 :::::::::::::::::::::::::: ::::::: :::::: ::::::: d1kica_ 1 -SAKNVVLDHAGNLDDFVAMVLLASNTekVRLIGALctdadcfvENGFNVtGKIMCLMhn 59 d1qyca_ 56 ----GANIVH----------------------------------------------GSID 65 :::::: :::: d1kica_ 60 nmnlPLFPIGksaatavnpfpkewrclaknmddmpilnipenvelwdkikaenekyEGQQ 119 d1qyca_ 66 dhaSLVEAVKN---vDVVISTVGslqIESQVNIIK-aIKEV-GTVKRFFPSEfgnDVDNV 120 :::::::: :::::::: ::::::::: :::: :::::::::: ::::: d1kica_ 120 ---LLADLVMNseekVTICVTGP---LSNVAWCIDkyGEKFtSKVEECVIMG---GAVDV 170 d1qyca_ 121 -----haVEPAKS--vfEVKAKVRRAIEAEG-IPYTYVSS---NCFAGyfLRSLaqaglt 169 :::::: :::::::::::::: :::::::: ::::: :::: d1kica_ 171 rgnvflpSTDGTAewniYWDPASAKTVFGCPgLRRIMFSLdstNTVPV--RSPY-vqrfg 227 d1qyca_ 170 apprdkvvilgdgnarvvFVKEedIGTFTIKAV--------------------------- 202 :::: ::::::::: d1kica_ 228 eqtnfllsilvgtmwamcTYYA--WDALTAAYVvdqkvanvdpvpidvvvdkqpnegatv 285 d1qyca_ 203 ---ddprtlNKTLylrlpantlslnelvalwekkidktlekayvpeeevlkliadtpfpa 259 :::: d1kica_ 286 rtdaenyplTFVA----------------------------------------------- 298 d1qyca_ 260 nisiaishsifvkgdqtnfeigpagVEASqlYPDVKYttvdeylsnfv 307 :::: :::::: d1kica_ 299 -------------------------RNPE--AEFFLD--mllrsarac 317 FAST alignment (Normalized score: 4.01 Raw score:1251.00) d1qyca_ 1 GSRSRILLIG--ATGYIGRHVAKASLDL---GHPT-FLLVRESTASS------NSEKAQL 48 ::::::: ::::::::::::::: :::: :::: ::::::: d1kica_ 1 -SAKNVVL--DHAGNLDDFVAMVLLAS-NTEKVRLIGALC-------TDADCFVENGFNV 49 d1qyca_ 49 -LESFKA----SGANIVHGSID-------------------------------------- 65 :::::: :::::: d1kica_ 50 TGKIMCLMHNNMNLPLF-----PIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVEL 104 d1qyca_ 66 ------------DHASLVEAVKNV----DVVISTVGSLQIE--SQVNIIKAIKEV----- 102 ::::::::::: ::::: :::::::::::: d1kica_ 105 WDKIKAENEKYEGQQLLADLVMN-SEEKVTICV--------TGPLSNVAWCIDKYGEKFT 155 d1qyca_ 103 GTVKRFFPSEFGNDVDNVHAVEPAKSVFEV--------------------------KAKV 136 :::::::: :::: d1kica_ 156 SKVEECVI----------------------MGGAVDVRGNVFLPSTDGTAEWNIYWDPAS 193 d1qyca_ 137 RRAIEA-EGIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARVVFVKEE--- 192 :::::: :::::::: d1kica_ 194 AKTVFGCPGLRRIMF------------------------------------------SLD 211 d1qyca_ 193 -------------------------------------DIGTFTIKAVDDPRTL------- 208 :::::::::::::: d1kica_ 212 STNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMCTYYAWDALTAAYVVDQK--VANVDPV 269 d1qyca_ 209 -------------------------NKTLYLRLPANTLSLNELVALWEKKIDKTLEKAYV 243 :::: d1kica_ 270 PIDVVVDKQPNEGATVRTDAENYPLTFVA------------------------------- 298 d1qyca_ 244 PEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAGVEASQLYPDVKYTTVDEYL 303 d1kica_ 299 ------------------------------------------------------------ 299 d1qyca_ 304 SNFV------------------- 307 d1kica_ 299 ----RNPEAEFFLDMLLRSARAC 317 TMalign alignment (TM-score: 0.40 Raw score:122.17) d1qyca_ 1 GSRSRILLIGATGY-IGRHVAKAS-LDLGHPTFLLVR---------ESTAS-SNSEKAQL 48 :::::::::::: ::::::::: :::::::::::: : ::::::: d1kica_ 1 --SAKNVVLDHAGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVE----NG-FNVTGKI 53 d1qyca_ 49 LESFKASGANIVHGSID------------------------------------------- 65 ::::::::::::::::: d1kica_ 54 MCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPENVELWDKIKAENE 113 d1qyca_ 66 -DHASLVEAVKNVDVVISTVGSLQIESQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVE 124 :::::::::::::: : ::::: ::::: : d1kica_ 114 K--------------------YEGQQLLADLVMNS--E--EKVTI-CVTGP-L------- 140 d1qyca_ 125 PAKSVFEVKAKVRR-AIEAE-GIPYTYVSSNCF----AGYFLRSLAQAGLTAPPRDKVVI 178 : ::::::: ::::: :::::::::::: : ::: :: d1kica_ 141 -----S-NVAWCIDKYGEKFTSKVEECVIMGGAVDVR----G--NVF-----------LP 177 d1qyca_ 179 LGDGNARV------------------------VF--V----------------------- 189 :: ::::: :: : d1kica_ 178 ST-DGTAEWNIYWDPASAKTVFGCPGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSI 236 d1qyca_ 190 -------------KEEDIGTFTIKAV-DD-PRTLNKTLY-LRLPANTLSLNELVALWEKK 233 ::::::::::::: : :: :::: d1kica_ 237 LVGTMWAMCTYYAWDALTAAYVVDQKV-AN-VD--PVPID-------------------- 272 d1qyca_ 234 IDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEI---GPAGVEASQL 290 :::::::::::::::: ::::::::: d1kica_ 273 -------------------------------VVVDKQPNEGATVRTDAENYPLTFVARN- 300 d1qyca_ 291 YPDVK-YT----------TVDEYLSNFV 307 :::: :: d1kica_ 301 -PEAEFFLDMLLRSARAC---------- 317 HHsearch alignment (Probability: 0.01 E-value:1.10) d1qyca_ 131 EVKAKVRRAIEAEGIPYTYVSSN 153 ::::::::::::::::::::::: d1kica_ 116 EGQQLLADLVMNSEEKVTICVTG 138