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: 542d3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.715 --> Intermediate <-- 1.453 --> Hit

SVM
score
SVM
score

The query (542d3.pdb) is transitively linked to the hit (d1igna1) through the intermediate protein (d1ri7a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ri7a1 Putative transcriptional regulator PH1519"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1igna1 DNA-​binding domain of rap1Homeodomain-​likeDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 0.715 --> Intermediate
DALI alignment (Z-score: 3.0 Raw score:159.80) query 1 pDYPVLDAILELYVDRD-TGADAIVAA-gYDRELVVKTLRMVDTAEykrrqyppgtkisa 58 :::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGkAPLREISKItgLAESTIHERIRKLRESG-----------vik 48 query 59 KGFGkdrrlpitnrwregh 77 :::: d1ri7a1 49 KFTA-------iidpealg 60 FAST alignment (Normalized score: 4.52 Raw score:307.00) query 1 PDYPVLDAILELYVDR-DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISA 58 ::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRE---------------- 43 query 59 KGFGKDRRLPITNRWREGH----------------- 77 d1ri7a1 44 -------------------SGVIKKFTAIIDPEALG 60 TMalign alignment (TM-score: 0.42 Raw score:32.51) query 1 PDYPVLDAILELYVDRD--TGADAIVAAGYDR-ELVVKTLRM-VDTAE--YKRRQYPPGT 54 :: :::::::::: ::: ::::::::::::: ::::::::: : ::: : d1ri7a1 1 LD-EIDKKIIKIL-QNDGKAPLREISKITGLAESTIHERIRKLR-ESGVI--K------- 48 query 55 KISAKGFGKDRR--------LPITNRWREGH 77 :: :: d1ri7a1 49 ------KF--TAIIDPEALG----------- 60 HHsearch alignment (Probability: 0.05 E-value:0.06) query 4 PVLDAILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTA 43 :::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 2 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES 44
Intermediate <-- 1.453 --> Hit
DALI alignment (Z-score: 4.7 Raw score:200.90) d1ri7a1 1 ----LDEIDKKIIKILQNDGKA-----PLREISKITG-LAESTIHERIR-KLREsgVIKK 49 :::::::::::::::::: :::::::::: ::::::::::: :::: :::: d1igna1 1 kasfTDEEDEFILDVVRKNPTRrtthtLYDEISHYVPnHTGNSIRHRFRvYLSK--RLEY 58 d1ri7a1 50 FTA-------IIDPE----------alg 60 ::: ::::: d1igna1 59 VYEvdkfgklVRDDDgnliktkvlppsi 86 FAST alignment (Normalized score: 5.11 Raw score:366.80) d1ri7a1 1 ----LDEIDKKIIKILQNDGKA-------PLREISKIT-GLAESTIHERIR-KLRESGVI 47 :::::::::::::::: ::::::::: :::::::::::: ::: ::: d1igna1 1 KASFTDEEDEFILDVVRKNP--TRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLS--KRL 56 d1ri7a1 48 KKFTAIIDPEALG------------------------ 60 :::::: d1igna1 57 EYVYEV-------DKFGKLVRDDDGNLIKTKVLPPSI 86 TMalign alignment (TM-score: 0.62 Raw score:36.95) d1ri7a1 1 ----LDEIDKKIIKILQNDG-KA----PLREISKITG-LAESTIHERIR-KLRESGVIKK 49 :::::::::::::::: :: :::::::::: ::::::::::: ::: ::::: d1igna1 1 KASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLS--KRLEY 58 d1ri7a1 50 F----------------------TAI--IDPEALG 60 : ::: d1igna1 59 VYEVDKFGKLVRDDDGNLIKTKVLPPSI------- 86 HHsearch alignment (Probability: 0.44 E-value:0.00) d1ri7a1 3 EIDKKIIKILQNDGK-----APLREISKIT-GLAESTIHERIRKLRESGVI 47 ::::::::::::::: :::::::::: :::::::::::::::::::: d1igna1 7 EEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSKRLE 57