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 <-- 0.855 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1hgxa_) 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 d1hgxa_ Hypoxanthine-​guanine-​xanthine PRTasePRTase-​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 <-- 0.855 --> Hit
DALI alignment (Z-score: 3.3 Raw score:270.50) d1gmxa_ 1 -------------mdqfeciNVADAHQKLQEKEAVLVDIRDPqsfamGHAV--------- 38 :::::::::::::::::::::: :::: d1hgxa_ 1 mddlervlynqddiqkrireLAAELTEFYEDKNPVMICVLTG---avFFYTdllkhldfq 57 d1gmxa_ 39 -qaFHLT-----NDTLgaFMRDNdFDTPVMVMCYH---gnSSKGAAQYLLQQGYDVVYSI 89 :::: :::: ::::: ::::::::::: :::::::::::::::::::: d1hgxa_ 58 lepDYIIcssltISKD--LKTNI-EGRHVLVVEDIidtglTMYQLLNNLQMRKPASLKVC 114 d1gmxa_ 90 dgGFEA--------------WQRQ-------------------fpaevayga 108 :::: :::: d1hgxa_ 115 --TLCDkdigkkaydvpidyCGFVvenryiigygfdfhnkyrnlpvigilke 164 FAST alignment (Normalized score: 3.80 Raw score:505.80) d1gmxa_ 1 MDQFECI--------------------NVADAHQKLQEKEAVLVDIR--DPQSFAMGHA- 37 :::::::::::::::::::: :::::: d1hgxa_ 1 -------MDDLERVLYNQDDIQKRIRELAAELTEFYEDKNPVMICVLTGAVFFYT----D 49 d1gmxa_ 38 --------VQAFHLTNDTLGAFMRDN--------------DFDTPVMVMCYH---GNSSK 72 :::::: :::::::::::: ::::: d1hgxa_ 50 LLKHLDFQLEPDYI------------ICSSLTISKDLKTNIEGRHVLVVEDIIDTGLTMY 97 d1gmxa_ 73 GAAQYLLQQGYDVVYSIDGGFEAWQRQFPAEVAYGA------------------------ 108 ::::::::::::::::: d1hgxa_ 98 QLLNNLQMRKPASLKVC-------------------TLCDKDIGKKAYDVPIDYCGFVVE 138 d1gmxa_ 109 -------------------------- 109 d1hgxa_ 139 NRYIIGYGFDFHNKYRNLPVIGILKE 164 TMalign alignment (TM-score: 0.52 Raw score:56.52) d1gmxa_ 1 --------------------MDQFECINV-ADAHQKLQEKE-AVLVDIRDPQSFAMGH-- 36 : ::::::: ::: :::::::: ::: ::: d1hgxa_ 1 MDDLERVLYNQDDIQKRIRE--------LAAELTEFY-EDKNPVMICVLT-GAV-FFYTD 49 d1gmxa_ 37 AV------Q-AFHLT-----N-DTLGAFMRDNDFDTPVMVMCYHG--N-SSKGAAQYLLQ 80 :: : ::::: : ::: ::: : :::::::::::: : ::::::::::: d1hgxa_ 50 LLKHLDFQLEPDYIICSSLTISKDL-KTN--I-EGRHVLVVEDIIDTGLTMYQLLNNLQM 105 d1gmxa_ 81 QGYDVVYSIDGGFE----------------AW---------------------------- 96 ::::::::: ::: :: d1hgxa_ 106 RKPASLKVC--TLCDKDIGKKAYDVPIDYCGFVVENRYIIGYGFDFHNKYRNLPVIGILK 163 d1gmxa_ 97 -QRQFPAEVAYGA 108 d1hgxa_ 164 E------------ 164 HHsearch alignment (Probability: 0.16 E-value:0.02) d1gmxa_ 12 AHQKLQEKEAVLVDIRDPQSFAMGHAVQAFHLT---------NDTLGAFMRDNDFDTPVM 62 ::::::::::::::::::::::::::::::::: :::::::::::::::::: d1hgxa_ 25 LTEFYEDKNPVMICVLTGAVFFYTDLLKHLDFQLEPDYIICSSLTISKDLKTNIEGRHVL 84 d1gmxa_ 63 VM---CYHGNSSKGAAQYLLQQGYDVVYSI 89 :: ::::::::::::::::::::::::: d1hgxa_ 85 VVEDIIDTGLTMYQLLNNLQMRKPASLKVC 114