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 <-- 0.724 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1pg4a_) 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 d1pg4a_ Acetyl-​CoA synthetaseAcetyl-​CoA synthetase-​likeAcetyl-​CoA synthetase-​likemulti

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 <-- 0.724 --> Hit
DALI alignment (Z-score: 6.7 Raw score:578.50) d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 1 hkhaipaniadrclinpeqyetkykqsindpdtfwgeqgkildwitpyqkvkntsfapgn 60 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 61 vsikwyedgtlnlaancldrhlqengdrtaiiwegddtsqskhisyrelhrdvcrfantl 120 d1qyca_ 1 -----GSRSRILLIGaTGYIGRHVAKASLDLGHPTFLLVrestassnsekaqllesfkas 55 :::::::::: ::::::::::::::::::::::: d1pg4a_ 121 ldlgiKKGDVVAIYMpMVPEAAVAMLACARIGAVHSVIF--------------------- 159 d1qyca_ 56 ganivhGSIDdHASLVEAVK--NVDVVIST-VGSL---QIESQVNIIKAIKE--VGTVKR 107 :::: ::::::::: :::::::: :::: :::::::::::::: :::::: d1pg4a_ 160 ------GGFS-PEAVAGCIIdsSSRLVITAdEGVRagrSIPLKKNVDDALKNpnVTSVEH 212 d1qyca_ 108 FFPSEfgndvdnvhavepaksvfeVKAKVrrAIEAegiPYTYVSsncfagyflrslaqag 167 ::::: ::::: :::: :::::: d1pg4a_ 213 VIVLK------------------rTGSDI--DWQE--gRDLWWR---------------- 234 d1qyca_ 168 ltapprdkvvilgdgnarvvfvkeedigtftikavddprtlnkTLYLrlpantlslnelv 227 :::: d1pg4a_ 235 -------------------------------------------DLIE------------- 238 d1qyca_ 228 alwekkidktlekayvpeeevlkliadtpfpanisiaishsifvkgdqtnfeigpagvEA 287 :: d1pg4a_ 239 ----------------------------------------------------------KA 240 d1qyca_ 288 SQLY-------------------------------------------------------- 291 :::: d1pg4a_ 241 SPEHqpeamnaedplfilytsgstgkpkgvlhttggylvyaattfkyvfdyhpgdiywct 300 d1qyca_ 292 ------------------------------------------------------------ 292 d1pg4a_ 301 advgwvtghsyllygplacgattlmfegvpnwptparmcqvvdkhqvnilytaptairal 360 d1qyca_ 292 ------------------------------------------------------------ 292 d1pg4a_ 361 maegdkaiegtdrsslrilgsvgepinpeawewywkkigkekcpvvdtwwqtetggfmit 420 d1qyca_ 292 ------------------------------------------------------------ 292 d1pg4a_ 421 plpgaielkagsatrpffgvqpalvdneghpqegategnlvitdswpgqartlfgdherf 480 d1qyca_ 292 ------------------------------------------------------------ 292 d1pg4a_ 481 eqtyfstfknmyfsgdgarrdedgyywitgrvddvlnvsghrlgtaeiesalvahpkiae 540 d1qyca_ 292 ------------------------------------------------------------ 292 d1pg4a_ 541 aavvgiphaikgqaiyayvtlnhgeepspelyaevrnwvrkeigplatpdvlhwtdslpk 600 d1qyca_ 292 -----------------pdvkyttvdeylsnfv 307 d1pg4a_ 601 trsgkimrrilrkiaagdadpgvveklleekqa 633 FAST alignment (Normalized score: 2.01 Raw score:887.00) d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 1 HKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGN 60 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 61 VSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRFANTL 120 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 121 LDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGCIIDSSSRLVI 180 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 181 TADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKA 240 d1qyca_ 1 ---------------------------------------------------GSRSRILL- 8 :::::::: d1pg4a_ 241 SPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCT 300 d1qyca_ 9 IGATGYIGRHV-AKASLDLGHPTFLLVRESTASSNSEKAQLLESFKASGANIVHGSID-- 65 ::::::::::: ::::::::::::: ::::: d1pg4a_ 301 ADVGWVTGHSYLLYGPLACGATTLM---------------------------FEGVP-NW 332 d1qyca_ 66 -DHASLVEAVK--NVDVVISTVGSLQIESQVNIIKAIK------------EVGTVKRFFP 110 :::::::::: :::::: :::::::: ::::::::: d1pg4a_ 333 PTPARMCQVVDKHQVNILY--TAPTAIRA---------LMAEGDKAIEGTDRSSLRILG- 380 d1qyca_ 111 SEFGNDVDNVHAVEPAKSVFEV-KAKVRRAIEA-----EGIPYTYVSSNCFAGYFLRSLA 164 ::::: ::::::::: :::::::::: d1pg4a_ 381 -SVGEP----------------INPEAWEWYW-KKIGKEKCPVVDTWW------------ 410 d1qyca_ 165 QAGLTAPPRDKVVILGDGNARVVFVKEEDIGTFTIKAVDDPRTLNKTLYLRLPANTLSLN 224 d1pg4a_ 411 ------------------------------------------------------------ 411 d1qyca_ 225 ELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGDQTNFEIGPAG 284 d1pg4a_ 411 ------------------------------------------------------------ 411 d1qyca_ 285 VEASQLYPDVKYTTVDEYLSNFV------------------------------------- 307 d1pg4a_ 411 -----------------------QTETGGFMITPLPGAIELKAGSATRPFFGVQPALVDN 447 d1qyca_ 308 ------------------------------------------------------------ 308 d1pg4a_ 448 EGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYW 507 d1qyca_ 308 ------------------------------------------------------------ 308 d1pg4a_ 508 ITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQAIYAYVTLNHGEEP 567 d1qyca_ 308 ------------------------------------------------------------ 308 d1pg4a_ 568 SPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDADPGVVEKL 627 d1qyca_ 308 ------ 308 d1pg4a_ 628 LEEKQA 633 TMalign alignment (TM-score: 0.41 Raw score:125.06) d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 1 HKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGN 60 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 61 VSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRFANTL 120 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 121 LDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGCIIDSSSRLVI 180 d1qyca_ 1 ------------------------------------------------------------ 1 d1pg4a_ 181 TADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKA 240 d1qyca_ 1 ---------------------------------------------------GSRSRILLI 9 ::::::::: d1pg4a_ 241 SPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCT 300 d1qyca_ 10 GAT-GYIGRHVA-KASLDLGHPTFLLVRESTASSNSEKAQLLESFKASGANIVHGSIDDH 67 ::: :::::::: ::::::::::::::: :::::: d1pg4a_ 301 ADVGWVTGHSYLLYGPLACGATTLMFEG--------------------------VPNWPT 334 d1qyca_ 68 -ASLVEAVK-NVDVVISTVGSLQIESQV-NII-KAIKEVGTVKRFFPSEFGNDVDNVHAV 123 :::::::: ::::::::::: :::::: ::: ::::::::::::::::::: d1pg4a_ 335 PARMCQVVDKHQVNILYTAPT-AIRALMAEGDKAIEGTDRSSLRILGSVGEP-------- 385 d1qyca_ 124 EPAKSVFEVKAKVRRAIEAE--GIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGD 181 :: :::::::::: :::::::::::::: d1pg4a_ 386 ------IN--PEAWEWYWKKIGKEKCPVVDTWWQTE------------------------ 413 d1qyca_ 182 GNARVVFVKEEDIGTFTIKAVDDPRTLNKT--LYLRL-PANTLSL---N-E--------- 225 :::::: :: : :::::::: ::::: ::::::: : : d1pg4a_ 414 --------TGGFMI-TP--L--PGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNL 460 d1qyca_ 226 LVALW---------------EKKI--DKTLEK-----AYVPEEEVLKLIADTPFPANISI 263 ::::: :: :::: d1pg4a_ 461 VITDSWPGQARTLFGDHERF--EQTY--FSTFKNMYF----------------------- 493 d1qyca_ 264 AISHSIFVKGDQTNFEIG-PAG-------------------------------------- 284 :: :: :: :::::: : d1pg4a_ 494 -SG--DG--AR-RDEDGYY--WITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVG 545 d1qyca_ 285 ------------------------------------------------------------ 285 d1pg4a_ 546 IPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGK 605 d1qyca_ 285 ----------------------------VEASQLYPDVKYTTVDEYLSNFV 307 d1pg4a_ 606 IMRRILRKIAAGDADPGVVEKLLEEKQA----------------------- 633 HHsearch alignment (Probability: 0.00 E-value:0.39) d1qyca_ 225 ELVALWEKKIDK 236 :::::::::::: d1pg4a_ 389 EAWEWYWKKIGK 400