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: T592_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.662 --> Intermediate <-- 0.863 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1a3ca_) through the intermediate protein (d1gmxa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gmxa_ Sulfurtransferase GlpERhodanese/​Cell cycle control phosphataseRhodanese/​Cell cycle control phosphataseα/β
Hit d1a3ca_ Pyrimidine operon regulator PyrRPRTase-​likePRTase-​likeα/β

Supporting Alignments

Query <-- 1.662 --> Intermediate
DALI alignment (Z-score: 13.4 Raw score:712.00) query 1 npneayrhymkklsYETDIADLSIDIKkgYEGIIVVDVRDAEAYKECHIPTAISIPgNKI 60 ::::::::::::: ::::::::::::::::::::::::::: ::: d1gmxa_ 1 ----------mdqfECINVADAHQKLQ--EKEAVLVDIRDPQSFAMGHAVQAFHLT-NDT 47 query 61 NEDTTKRLSKEKVIITYCWGpacNGATKAAAKFAQLGF-RVKELIGGIEYWRKENG-EVE 118 :::::::::::::::::::: ::::::::::::::: ::::::::::::::::: ::: d1gmxa_ 48 LGAFMRDNDFDTPVMVMCYH--gNSSKGAAQYLLQQGYdVVYSIDGGFEAWQRQFPaEVA 105 query 119 GTlgakadlfwnmkkesle 137 :: d1gmxa_ 106 YG----------------a 108 FAST alignment (Normalized score: 11.37 Raw score:1383.00) query 1 NPNEAYRHYMKKLS----YETDIADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIP 56 :::::::::::::: :::::::::::::::::::::::::: d1gmxa_ 1 --------------MDQFECINVADAHQKLQE--KEAVLVDIRDPQSFAMGHAVQAFHLT 44 query 57 GNKINEDTTKRLSKEKVIITYCWGPACNGATKAAAKFAQLG-FRVKELIGGIEYWRKENG 115 ::: ::::::::::::::::::::: :::::::::::::: ::::::::::::::: d1gmxa_ 45 NDT-LGAFMRDNDFDTPVMVMCYHG--NSSKGAAQYLLQQGYDVVYSIDGGFEAWQR--- 98 query 116 EVEGTLGAKADLFWNMKKESLE---------- 137 d1gmxa_ 99 ----------------------QFPAEVAYGA 108 TMalign alignment (TM-score: 0.65 Raw score:88.83) query 1 --NPNEAYRHYMKKLSYETDIADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIPGN 58 : ::::::::::::: :::::::::::::::::::::::::::: d1gmxa_ 1 MD-----------Q-FECINVADAHQKL--QEKEAVLVDIRDPQSFAMGHAVQAFHLT-- 44 query 59 KINEDT-TKRLSKEKVIITYCWGPACNGATKAAAKFAQLGF-RVKELIGGIEYWRKENG- 115 :::::: ::::::::::::::::: ::::::::::::::: ::::::::::::::::: d1gmxa_ 45 NDTLGAFMRDNDFDTPVMVMCYHG--NSSKGAAQYLLQQGYDVVYSIDGGFEAWQRQFPA 102 query 116 EVEGT-LGAKADLFWNMKKESLE 137 ::::: d1gmxa_ 103 EVAYGA----------------- 108 HHsearch alignment (Probability: 1.00 E-value:0.00) query 16 ETDIADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIPGNKINEDTTKRLSKEKVII 75 ::::::::::::: :::::::::::::::::::::::::::::: :::::::::::::: d1gmxa_ 6 CINVADAHQKLQE--KEAVLVDIRDPQSFAMGHAVQAFHLTNDTL-GAFMRDNDFDTPVM 62 query 76 TYCWGPACNGATKAAAKFAQLGFR-VKELIGGIEYWRKENGEVEGTLGA 123 :::::: :::::::::::::::: :::::::::::::: ::::::::: d1gmxa_ 63 VMCYHG--NSSKGAAQYLLQQGYDVVYSIDGGFEAWQRQ-FPAEVAYGA 108
Intermediate <-- 0.863 --> Hit
DALI alignment (Z-score: 2.9 Raw score:254.00) d1gmxa_ 1 ------mdqfecinvadaHQKLQEKE-AVLVDIRDpqsfamgHAVQ------------aF 41 :::::::: :::::::: :::: : d1a3ca_ 1 qkavildeqairraltriAHEMIERNkCILVGIKT-rgiylaKRLAerieqiegnpvtvG 59 d1gmxa_ 42 HLT-----------NDTLgaFMRDNdFDTPVMVMCYH---gNSSKGAAQYLLQQGYD-VV 86 ::: :::: ::::: ::::::::::: :::::::::::::::: :: d1a3ca_ 60 EIDitlyrndeplvKGAD--IPVDI-TDQKVILVDDVlytgRTVRAGMDALVDVGRPsSI 116 d1gmxa_ 87 YSIdgGFEA------------WQRQ------------------fpaevayga 108 ::: :::: :::: d1a3ca_ 117 QLA--VLVDrghrelpiradyIGKNiptsksekvmvqldevdqndlvaiyen 166 FAST alignment (Normalized score: 3.21 Raw score:429.60) d1gmxa_ 1 MDQFECI-------------NVADAHQKLQEK--EAVLVDIRDPQSFAMGHA-------- 37 ::::::::::: :::::::: d1a3ca_ 1 -------QKAVILDEQAIRRALTRIAHEMIE-RNKCILVGIK----------TRGIYLAK 42 d1gmxa_ 38 -------------VQAFHLTNDTLGAFMRDND---------------------FDTPVMV 63 :::::: ::::::: d1a3ca_ 43 RLAERIEQIEGNPVTVGEI-------------DITLYRNDEPLVKGADIPVDITDQKVIL 89 d1gmxa_ 64 MCYH---GNSSKGAAQYLLQ-QGYDVVYSIDGGFEAWQRQFPAEVAYGA----------- 108 :::: ::::::::::::: ::::::::: d1a3ca_ 90 VDDVLYTGRTVRAGMDALVDVGRPSSIQLA-------------------VLVDRGHRELP 130 d1gmxa_ 109 ------------------------------------ 109 d1a3ca_ 131 IRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 166 TMalign alignment (TM-score: 0.52 Raw score:56.24) d1gmxa_ 1 ----------------MDQFECINVADAHQKLQEKE-AVLVDIRDPQSFAMGH--AVQA- 40 ::::: ::::: :::::::: ::: :: :::: d1a3ca_ 1 QKAVILDEQAIRRALT---------RIAHE-MIERNKCILVGIKT--RGI-YLAKRLAER 47 d1gmxa_ 41 ----------FHLTN------------DTLGAFMRDNDFDTPVMVMC-YHG-N-SSKGAA 75 ::::: ::: : ::::::::::::: ::: : :::::: d1a3ca_ 48 IEQIEGNPVTVGEIDITLYRNDEPLVKGAD--I-PVDITDQKVILVDDVLYTGRTVRAGM 104 d1gmxa_ 76 QYLLQQGYDVVYSIDGGFEA------------WQRQ------------FPAEVAYGA--- 108 ::::::::::::::: :::: :::: :::: d1a3ca_ 105 DALVDVGRPSSIQLA-VLVDRGHRELPIRADYIGKNIPTSKSEKVMVQ-----LDEVDQN 158 d1gmxa_ 109 -------- 109 d1a3ca_ 159 DLVAIYEN 166 HHsearch alignment (Probability: 0.01 E-value:0.34) d1gmxa_ 56 DFDTPVMVMC---YHGNSSKGAAQYLLQQGYDV 85 :::::::::: :::::::::::::::::::: d1a3ca_ 82 ITDQKVILVDDVLYTGRTVRAGMDALVDVGRPS 114