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 <-- 0.622 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1u2xa_) 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 d1u2xa_ ADP-​specific phosphofructokinaseRibokinase-​likeRibokinase-​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 <-- 0.622 --> Hit
DALI alignment (Z-score: 7.8 Raw score:924.70) d1qyca_ 1 --GSRSRILLIGAT---------------------------------------------- 12 :::::::::::: d1u2xa_ 1 miPEHLSIYTAYNAnidaivklnqetiqnlinafdpdevkrrieeypreinepidfvarl 60 d1qyca_ 13 ----------------------------------GYIGRHVAKASLDLGH-PTFLLVREs 37 :::::::::::::::: :::::::: d1u2xa_ 61 vhtlklgkpaavplvnekmnewfdktfryeeerlGGQAGIIANTLAGLKIrKVIAYTPF- 119 d1qyca_ 38 tassnseKAQLLESFKaSGANIVH------------------------------------ 61 ::::::::: ::::::: d1u2xa_ 120 ------lPKRLAELFK-KGVLYPVvengelqfkpiqeayregdplkinrifefrkglkfk 172 d1qyca_ 62 -------------------------gSIDD--HASLVEAVKNVDVVISTVGSL------- 87 :::: ::::::::::::::::::::: d1u2xa_ 173 lgdetieipnsgrfivsarfesisriETREdiKPFLGEIGKEVDGAIFSGYQGlrtkysd 232 d1qyca_ 88 ------QIESQVNIIKAIKeVGTVkRFFPSEFGndvdnvhavePAKSVFEVKAK-VRRAI 140 ::::::::::::: :::: :::::::: ::::::::::: ::::: d1u2xa_ 233 gkdanyYLRRAKEDIIEFK-EKDV-KIHVEFAS---------vQDRKLRKKIITnILPFV 281 d1qyca_ 141 eaegipYTYVSSNCfagyflrslaqagltapprdkvvilgdgNARVvfvkeedigtftik 200 :::::::: :::: d1u2xa_ 282 ------DSVGIDEA---------eiaqilsvlgyreladrifTYNR-----ledsilggm 321 d1qyca_ 201 avddprtLNKTLYLRLPantlslnelvalwekkidktlekayvpeeevlkliadtpfpan 260 :::::::::: d1u2xa_ 322 iildelnFEILQVHTTY------------------------------------------- 338 d1qyca_ 261 isiaishsifvkgdqtnfeIGPA-------gveasQLYP---DVKY-------------- 296 :::: :::: :::: d1u2xa_ 339 -----------------ylMYIThrdnplseeelaKSLEfgtTLAAaraslgdirgpddy 381 d1qyca_ 297 --------------------------------------TTVDEY---------------- 302 :::::: d1u2xa_ 382 kvglkvpfnerseyvklrfeeaksrlrmreykvvviptRLVQNPvltvglgdtisagafl 441 d1qyca_ 303 ----lsnfv 307 d1u2xa_ 442 tyleflkrh 450 FAST alignment (Normalized score: 2.54 Raw score:946.10) d1qyca_ 1 --GSRSRILLIGATG--------------------------------------------- 13 ::::::::: d1u2xa_ 1 MIPEHLSIYTA----YNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDF 56 d1qyca_ 14 ---------------------------------------YIGRHVAKASLDLGH-PTFLL 33 ::::::::::::::: ::::: d1u2xa_ 57 VARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAY 116 d1qyca_ 34 VRESTASSNSE---KAQLLESFKA--SGANIVHGSID----------------------- 65 : ::::::: ::::: d1u2xa_ 117 T----------PFLPKRLAEL---FKKGVLY------PVVENGELQFKPIQEAYREGDPL 157 d1qyca_ 66 ----------------------------------------------DHASLVEAVKNVDV 79 :::::::::::::: d1u2xa_ 158 KINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDG 217 d1qyca_ 80 VISTVGSLQIESQVNIIKAIKEVGTVKRFFPSEFGNDVDNVHAVE-------------PA 126 :::: :: d1u2xa_ 218 AIFS-----------------------------------------GYQGLRTKYSDGKDA 236 d1qyca_ 127 KSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYFLRSLAQAGLTAPPRDKVVILGDGNARV 186 :::::::::::::::::::::::::: d1u2xa_ 237 NYYLRRAKEDIIEFKEKDVKIHVEFA---------------------------------- 262 d1qyca_ 187 VFVKEEDIGTFTIKAVDDPRTL-------------------NKTLYLRLPANTL------ 221 ::::: d1u2xa_ 263 ----------------------SVQDRKLRKKIITNILPFVDSVGI--------DEAEIA 292 d1qyca_ 222 -------SLNELVALWEKKIDKTLEKAYVPEEEVLKLIADTPFPANISIAISHSIFVKGD 274 :::::::::: d1u2xa_ 293 QILSVLGYRELADRIFT------------------------------------------- 309 d1qyca_ 275 QTNFEIGP---------------------AGVEASQLYPDVKYTTVDEYLSNFV------ 307 :::: d1u2xa_ 310 --------YNRLEDSILGGMIILDELNFEILQV---------------------HTTYYL 340 d1qyca_ 308 ------------------------------------------------------------ 308 d1u2xa_ 341 MYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRF 400 d1qyca_ 308 -------------------------------------------------- 308 d1u2xa_ 401 EEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450 TMalign alignment (TM-score: 0.41 Raw score:125.37) d1qyca_ 1 -GSRSRILLIGATG---------------------------------------------- 13 ::::::::::::: d1u2xa_ 1 MIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARL 60 d1qyca_ 14 -----------------------------------YIGRHVAKASLDLGHPTFLLVR-ES 37 :::::::::::::::::::::: : d1u2xa_ 61 VHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTP-F 119 d1qyca_ 38 TASSNSEKAQLLESFKASGANIVHGSID-DHASLVEA----------------------- 73 : :::::::: :: :::::::: ::::: :: d1u2xa_ 120 -L--PKRLAELF--KK----GVLYPVVENGELQF-KPIQEAYREGDPLKINRIFEFRKGL 169 d1qyca_ 74 --------------------------VKNVDVVISTVGSLQIE-SQVNIIKAIKEVGTVK 106 ::::::: ::::::::: : :: d1u2xa_ 170 KFKLGDETIEIPNSGRFIVSARFESI----------SRIETREDIKPFLGEIG---K-EV 215 d1qyca_ 107 RFFPSEFGN---DVDNVHAV----EPAKSVFEVKAKVRRAIEAEGIPYTYVSSNCFAGYF 159 ::::::::: :: :::::::::::::::::: :::::::::::: : d1u2xa_ 216 DGAIFSGYQGLR------TKYSDGKDANYYLRRAKEDIIEFK--EKDVKIHVEFAS---V 264 d1qyca_ 160 LRSLAQAGLTAPPRDKVVILG-DGNAR--------VVFVKEEDIGTFTIKAVDDPRTLNK 210 : : :: :: :: d1u2xa_ 265 ----Q-D------------RKL---RKKIITNILP-----------------------FV 281 d1qyca_ 211 TLYLRLPANTLS--L-------NELVALW--------EKKIDKTLEKAYVPEEEVLKLIA 253 :::::::::::: : ::::::: d1u2xa_ 282 DSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSIL----------------------- 318 d1qyca_ 254 DTPFPANISIAISHSIFVKG-DQTNFEIGPAGVEA-------SQ------------L--Y 291 : ::::::::::::: :: : : d1u2xa_ 319 -------------------GG-MIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKS 358 d1qyca_ 292 PD-VK--Y---T------------------------------------------------ 297 :: :: : : d1u2xa_ 359 LEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIP 418 d1qyca_ 298 T---VDEY---LSN----------------------FV 307 : :: : d1u2xa_ 419 TRLV--QNPVL--TVGLGDTISAGAFLTYLEFLKRH-- 450 HHsearch alignment (Probability: 0.01 E-value:0.41) d1qyca_ 186 VVFVKEEDIGTFTIKAVDD 204 ::::::::::::::::::: d1u2xa_ 308 FTYNRLEDSILGGMIILDE 326