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 <-- 0.999 --> Intermediate <-- 0.999 --> Hit

HHsearch
probability
HHsearch
probability

The query (T592_B.pdb B) is transitively linked to the hit (d1t3ka_) through the intermediate protein (d1gmxa_) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1gmxa_ Sulfurtransferase GlpERhodanese/​Cell cycle control phosphataseRhodanese/​Cell cycle control phosphataseα/β
Hit d1t3ka_ Dual specificity phosphatase Cdc25Rhodanese/​Cell cycle control phosphataseRhodanese/​Cell cycle control phosphataseα/β

Supporting Alignments

Query <-- 0.999 --> 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 <-- 0.999 --> Hit
DALI alignment (Z-score: 4.3 Raw score:287.10) d1gmxa_ 1 ---mdQFECINvadahqklqEKEAVLVDIRDPQSFA--MGHAvqAFHLTN----DTLGAF 51 :::::: :::::::::::::::: :::: :::::: :::::: d1t3ka_ 1 mamarSISYITstqllplhrRPNIAIIDVRDEERNYdgHIAG--SLHYASgsfdDKISHL 58 d1gmxa_ 52 MRDNDfDTPVMVMCYHG-NSSKGAAQYLLQQG--------ydVVYSIDGGFEAWQRQFP- 101 ::::: ::::::::::: :::::::::::::: ::::::::::::::::: d1t3ka_ 59 VQNVKdKDTLVFHSALSqVRGPTCARRLVNYLdekkedtgikNIMILERGFNGWEASGKp 118 d1gmxa_ 102 --------aEVAYGa 108 ::::: d1t3ka_ 119 vcrcaevpcKGDCA- 132 FAST alignment (Normalized score: 4.50 Raw score:537.80) d1gmxa_ 1 MD-----QFECINVADAHQKLQ---EKEAVLVDIRDPQSFAMGHA-----VQAFHL---- 43 :::::::::::: ::::::::::::::: :::::: d1t3ka_ 1 --MAMARSISYITSTQLLP---LHRRPNIAIIDVRDEERN-----YDGHIAGSLHYASGS 50 d1gmxa_ 44 TNDTLGAFMRDNDFDTPVMVMCYH------GNSSKGAAQYLLQQ---------GYDVVYS 88 ::::::::::::::::::: ::::::::::::: ::::::: d1t3ka_ 51 FDDKISHLVQNVKDKDTLV-----FHSALSQVRGPTCARRLVN-YLDEKKEDTGIKNIMI 104 d1gmxa_ 89 IDGGFEA---WQRQFPAEVAYGA----------------- 108 :::: :::: d1t3ka_ 105 LERG---FNGWEAS---------GKPVCRCAEVPCKGDCA 132 TMalign alignment (TM-score: 0.58 Raw score:62.55) d1gmxa_ 1 ----MDQFECINVA-DA-HQKLQEKEAVLVDIRDP-QSFAMGHAVQAFHL-T--N-DTLG 49 ::::::::: :: ::: :::::::::::: ::::::::: :::: : : :::: d1t3ka_ 1 MAMA-RSISYITSTQLLP-LHR-RPNIAIIDVRDEERNYDGHIAG-SLHYASGSFDDKIS 56 d1gmxa_ 50 AFMRDNDFDTPVMVMCYHG-NSSKGAAQ-YL--L----QQG-YDVVYSIDGGFEAWQ--R 98 ::::::::::::::::::: :::::::: :: : ::: ::::::::::::: : : d1t3ka_ 57 HLVQNVKDKDTLVFHSALSQVRGPTCARRLVNYLDEKKEDTGIKNIMILERGFNG-WEAS 115 d1gmxa_ 99 Q---FP------AEVAYGA 108 : : :::::: d1t3ka_ 116 GKPV-CRCAEVPCKGDCA- 132 HHsearch alignment (Probability: 1.00 E-value:0.00) d1gmxa_ 2 DQFECINVADAHQKLQEKEAVLVDIRDPQSFAMGHAVQAFHLTNDTLGAFMRDND----F 57 ::::::::::::::::::::::::::::::::::::::::::::::::::::::: : d1t3ka_ 5 RSISYITSTQLLPLHRRPNIAIIDVRDEERNYDGHIAGSLHYASGSFDDKISHLVQNVKD 64 d1gmxa_ 58 DTPVMVMCYHGN-SS--------KGAAQYLLQQGYDVVYSIDGGFEAWQR-QFPAE 103 :::::::::::: :: ::::::::::::::::::::::::::: ::::: d1t3ka_ 65 KDTLVFHSALSQVRGPTCARRLVNYLDEKKEDTGIKNIMILERGFNGWEASGKPVC 120