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 <-- 0.886 --> Intermediate <-- 1.571 --> Hit

SVM
score
SVM
score

The query (542d3.pdb) is transitively linked to the hit (d1sfxa_) through the intermediate protein (d1on2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1on2a1 Manganese transport regulator MntR"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1sfxa_ Hypothetical protein AF2008"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 0.886 --> Intermediate
DALI alignment (Z-score: 1.6 Raw score:124.40) query 1 pDYPVLDAILELYVDRD-----TGADAIVAA-GYDRElvvKTLRMVDtaeykrrqyppgt 54 :::::::::::::::: ::::::::: ::::: ::::::: d1on2a1 1 -TTPSMEMYIEQIYMLIeekgyARVSDIAEAlAVHPSsvtKMVQKLD------------- 46 query 55 kisakgfgkdrrlpitnrwregh 77 d1on2a1 47 --------kdeyliyekyrglvl 61 FAST alignment (Normalized score: 4.60 Raw score:315.00) query 1 PDYPVLDAILELYVD-----RDTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGT 54 :::::::::::::: :::::::::: ::::::::::::::::: d1on2a1 1 -TTPSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDK------------ 47 query 55 KISAKGFGKDRRLPITNRWREGH-------------- 77 d1on2a1 48 -----------------------DEYLIYEKYRGLVL 61 TMalign alignment (TM-score: 0.41 Raw score:31.75) query 1 -PDYPVL-DAILELYVDR-D-----TGADAIVAA-GYDRELVVKTLRMVDTAEYKRRQYP 51 :: : ::::::: :: : ::::::::: :::::::::::::::::: d1on2a1 1 T-TP--SMEMYIEQI-YMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDE------- 49 query 52 PGTKISAKGFGKDRRLPITN-RW---RE--GH 77 : :: : : : d1on2a1 50 ---------Y----LI---YE-KYRG-LVL-- 61 HHsearch alignment (Probability: 0.04 E-value:0.09) query 4 PVLDAILELYVDRD-TGADAIVAA-GYDRELVVKTLRMVDTAEY 45 :::::::::::::: ::::::::: ::::::::::::::::::: d1on2a1 7 MYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEY 50
Intermediate <-- 1.571 --> Hit
DALI alignment (Z-score: 8.3 Raw score:278.10) d1on2a1 1 -----------------TTPSMEMYIEQIYMLIeekgYARVSDIAEALAVHPSSVTKMVQ 43 :::::::::::::::: ::::::::::::::::::::::: d1sfxa_ 1 hmsnplgelvkaleklsFKPSDVRIYSLLLERG----GMRVSEIARELDLSARFVRDRLK 56 d1on2a1 44 KLDKDEYLIYEKY------RGLVL----------------------------- 61 ::::::::::::: ::::: d1sfxa_ 57 VLLKRGFVRREIVekgwvgYIYSAekpekvlkefkssilgeieriekmftdgs 109 FAST alignment (Normalized score: 6.00 Raw score:489.20) d1on2a1 1 TTPSM------------------EMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMV 42 ::::::::::::::::::::::::::::::::::::: d1sfxa_ 1 -----HMSNPLGELVKALEKLSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRL 55 d1on2a1 43 QKLDKDEYLIYEKYRGLVL----------------------------------------- 61 :::::::::::: d1sfxa_ 56 KVLLKRGFVRRE-------IVEKGWVGYIYSAEKPEKVLKEFKSSILGEIERIEKMFTDG 108 d1on2a1 62 - 62 d1sfxa_ 109 S 109 TMalign alignment (TM-score: 0.74 Raw score:44.94) d1on2a1 1 ----------------TT-PSMEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQ 43 :: :::::::::::::: ::::::::::::::::::::::: d1sfxa_ 1 HMSNPLGELVKALEKLSFKPSDVRIYSLLLERG----GMRVSEIARELDLSARFVRDRLK 56 d1on2a1 44 KLDKDEYLIYEKY------RGLVL----------------------------- 61 ::::::::::::: ::::: d1sfxa_ 57 VLLKRGFVRREIVEKGWVGYIYSAEKPEKVLKEFKSSILGEIERIEKMFTDGS 109 HHsearch alignment (Probability: 0.98 E-value:0.00) d1on2a1 11 QIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY 56 :::::::::::::::::::::::::::::::::::::::::::::: d1sfxa_ 24 RIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV 69