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 <-- 2.077 --> Intermediate <-- 0.632 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1i9sa_) through the intermediate protein (d1qb0a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1qb0a_ CDC25bRhodanese/​Cell cycle control phosphataseRhodanese/​Cell cycle control phosphataseα/β
Hit d1i9sa_ mRNA capping enzyme,​ triphosphatase domain(Phosphotyrosine protein) phosphatases II(Phosphotyrosine protein) phosphatases IIα/β

Supporting Alignments

Query <-- 2.077 --> Intermediate
DALI alignment (Z-score: 11.9 Raw score:831.00) query 1 npneayRHYMK-----------------klsYETDIADLSIDIKKGY----EGIIVVDVR 39 ::::: :::::::::::::::: ::::::::: d1qb0a_ 1 ------DHRELigdyskafllqtvdgkhqdlKYISPETMVALLTGKFsnivDKFVIVDCR 54 query 40 DAEAYKECHIPTAISIPGN-KINEdTTKR-LSKE------KVIITYCWGpaCNGATKAAA 91 ::::::::::::::::::: :::: :::: :::: ::::::::: ::::::::: d1qb0a_ 55 YPYEYEGGHIKTAVNLPLErDAES-FLLKsPIAPcsldkrVILIFHCEF-sSERGPRMCR 112 query 92 KFAQLG-----------fRVKELIGGIEYWRKENG-EVEGtlgAKADlFWNMKKESLE-- 137 :::::: ::::::::::::::::: :::: :::: :::::::::: d1qb0a_ 113 FIRERDravndypslyypEMYILKGGYKEFFPQHPnFCEP---QDYR-PMNHEAFKDElk 168 query 138 --------- 138 d1qb0a_ 169 tfrlktrsw 177 FAST alignment (Normalized score: 8.06 Raw score:1255.00) query 1 NPNEAYRHYMKKLS-------------------------YETDIADLSIDIKKGYE---- 31 :::::::::::: d1qb0a_ 1 --------------DHRELIGDYSKAFLLQTVDGKHQDLKYISPETMVALL-----TGKF 41 query 32 -----GIIVVDVRDAEAYKECHIPTAISI-PGNKINEDTTKRLSK--------------- 70 :::::::::::::::::::::::: ::::: d1qb0a_ 42 SNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDA----------ESFLLKSPIAPCSLD 91 query 71 -EKVIITYCWGPA---CNGATKAAAKFAQLG-------------FRVKELIGGIEYWRKE 113 :::::::: ::::::::::::: ::::::::::::::: d1qb0a_ 92 KRVILIFHC----EFSSERGPRMCRFIRE--RDRAVNDYPSLYYPEMYILKGGYKEFFP- 144 query 114 NGEVEGTL-------GAKADLFW------NMKKESLE-------- 137 ::::: ::::::: d1qb0a_ 145 --------QHPNFCEPQDYR---PMNHEAFKDELKT-FRLKTRSW 177 TMalign alignment (TM-score: 0.73 Raw score:100.46) query 1 NPNEAYRHYMK-----------KL-------SYETDIADLSIDIKKG-Y---EGIIVVDV 38 :: :: :: :::::::::::::::: : :::::::: d1qb0a_ 1 -----DH--RELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDC 53 query 39 RDAEAYKECHIPTAISIPGNKINEDTT-KRLSKE------KVIITYCWGPACNGATKAAA 91 ::::::::::::::::::::::::::: :::::: :::::::::: ::::::::: d1qb0a_ 54 RYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHCEFS-SERGPRMCR 112 query 92 KFAQLG----------FR-VKELIGGIEYWRKENGE-VEGTLGAKADLFWNMKKESLE-- 137 :::::: :: ::::::::::::::::: :: ::::: :::::::::: d1qb0a_ 113 FIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCE---PQDYR-PMNHEAFKDELK 168 query 138 --------- 138 d1qb0a_ 169 TFRLKTRSW 177 HHsearch alignment (Probability: 0.99 E-value:0.00) query 17 TDIADLSIDIKK----GYEGIIVVDVRDAEAYKECHIPTAISIPGNKINEDTT------- 65 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1qb0a_ 28 ISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAP 87 query 66 KRLSKEKVIITYCWGPACNGATKAAAKFAQLGF-----------RVKELIGGIEYWRKE 113 ::::::::::::::::: ::::::::::::::: ::::::::::::::: d1qb0a_ 88 CSLDKRVILIFHCEFSS-ERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQ 145
Intermediate <-- 0.632 --> Hit
DALI alignment (Z-score: 2.7 Raw score:337.80) d1qb0a_ 1 dhreligdyskafllqtVDGK------------------------hqdlkyiSPETMVAL 36 :::: :::::::: d1i9sa_ 1 -----------kipprwLNCPrrgqpvagrflplktmlgprydsqvaeenrfHPSMLSNY 49 d1qb0a_ 37 LtGKFSniVDKFVIVDCRYpyeYEGGHIK--------TAVNLP-----------LERDAE 77 : :::: ::::::::::: ::::::: :::::: :::::: d1i9sa_ 50 L-KSLK--VKMSLLVDLTN---TSRFYDRndiekegiKYIKLQckghgecptteNTETFI 103 d1qb0a_ 78 SFLLKspiapcsldkRVILIFHCEFSSERGPRMCRFIRERDRAvndypslyypemyilkg 137 ::::: :::::::::::::::::::::::::::: d1i9sa_ 104 RLCER---------fPELIGVHCTHGFNRTGFLICAFLVEKMD-----wsieaavatfaq 149 d1qb0a_ 138 gykeffpqhpnfcepqdyrpmnheafkdelktfrlktrsw 177 d1i9sa_ 150 arppgiykgdylkelfrrygdieeappppvlpdwcfeded 189 FAST alignment (Normalized score: 2.83 Raw score:517.20) d1qb0a_ 1 DHRELIGDYSKAFLLQTVDGKHQDLKY--------------------------------- 27 d1i9sa_ 1 ---------------------------KIPPRWLNCPRRGQPVAGRFLPLKTMLGPRYDS 33 d1qb0a_ 28 -------ISPETMVALLTGKFSNIVDK------FVIVDCRYPYEYEGGHI---------- 64 ::::::::::: :::::::: d1i9sa_ 34 QVAEENRFHPSMLSNYLK---------SLKVKMSLLVDLTN---------TSRFYDRNDI 75 d1qb0a_ 65 ----KTAVNLP------------LERDAESFLLKSPIAPCSLDK--RVILIFHCEFSSER 106 :::::: :::::::::: :::::::::::::: d1i9sa_ 76 EKEGIKYIKL-QCKGHGECPTTENTETFIRLCE-----------RFPELIGVHCTHGFNR 123 d1qb0a_ 107 GPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDE 166 :::::::::::: d1i9sa_ 124 TGFLICAFLVEK------------------------------------------------ 135 d1qb0a_ 167 LKTFRLKTRSW------------------------------------------------- 177 d1i9sa_ 136 -----------MDWSIEAAVATFAQARPPGIYKGDYLKELFRRYGDIEEAPPPPVLPDWC 184 d1qb0a_ 178 ----- 178 d1i9sa_ 185 FEDED 189 TMalign alignment (TM-score: 0.39 Raw score:69.24) d1qb0a_ 1 ------------DHRELIGDYSKAFLLQTVDGKHQDLKYISP------------ETMVAL 36 ::::: :: :: :::::: :::::: d1i9sa_ 1 KIPPRWLNCPRR---GQPVA-GR-FL----------PLKTMLGPRYDSQVAEENRFHPSM 45 d1qb0a_ 37 LTGK-FS--NI-VDKFVIVDCRYPYEYEGGHIKT----------AVNLPL-----ER-DA 76 : :: :: :: :::::::: : :: ::::: :::::: :: :: d1i9sa_ 46 L-SNYLKSLKVKMSLLVDLT-N----TS-RFYDRNDIEKEGIKYIKLQCKGHGECPTTEN 98 d1qb0a_ 77 ESFLLKSPIAPCSLDKRVILIFHCEFSSERGPRMCRFIRERDRAV-NDYP--SL--YYPE 131 ::::::::::: : :::::::: : ::::::::::::::: :::: :: :: d1i9sa_ 99 TETFIRLCERF--P-ELIGVHCT---H---GFNRTGFLICAFLVEKMDWSIEAAVA--TF 147 d1qb0a_ 132 --MYI-------------------------------------LKGGYKEFFPQHPNFCEP 152 ::: d1i9sa_ 148 AQARPPGIYKGDYLKELFRRYGDIEEAPPPPVLPDWCFEDED------------------ 189 d1qb0a_ 153 QDYRPMNHEAFKDELKTFRLKTRSW 177 d1i9sa_ 190 ------------------------- 190 HHsearch alignment (Probability: 0.56 E-value:0.00) d1qb0a_ 26 KYISPETMVALLTGKFSNIVDKFVIVDCRY------PYEYEGGHIKT------AVN-LPL 72 :::::::::::::: ::::::::::::: ::::::::::: ::: ::: d1i9sa_ 39 NRFHPSMLSNYLKS---LKVKMSLLVDLTNTSRFYDRNDIEKEGIKYIKLQCKGHGECPT 95 d1qb0a_ 73 ERDAESFLLKSPIAPCSLDKRVILIFHCEFSSERGPRM-CRFIRERDRAVNDYPSLYYPE 131 ::::::::::: ::::::::::::::::::::: ::::::::: d1i9sa_ 96 TENTETFIRLC------ERFPELIGVHCTHGFNRTGFLICAFLVEKMD------------ 137 d1qb0a_ 132 MYILKGGYKEFFPQHPNFCEPQDYR 156 :::::::::::::::::::::::: d1i9sa_ 138 -WSIEAAVATFAQARPPGIYKGDYL 161