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
SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
---|---|---|---|---|---|
Intermediate | d1on2a1 | Manganese transport regulator MntR | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
Hit | d1sd4a_ | Penicillinase repressor BlaI | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α |
Query <-- 0.886 --> IntermediateDALI 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 <-- 2.516 --> HitDALI alignment (Z-score: 7.1 Raw score:247.40) d1on2a1 1 ---TTPSMEMYIEQIYMLIeekgYARVSDIAEALA----VHPSSVTKMVQKLDKDEYLIY 53 :::::::::::::::: :::::::::::: ::::::::::::::::::::: d1sd4a_ 1 qveISMAEWDVMNIIWDKK----SVSANEIVVEIQkykeVSDKTIRTLITRLYKKEIIKR 56 d1on2a1 54 EKY---RGLVL------------------------------------------------- 61 ::: ::::: d1sd4a_ 57 YKSeniYFYSSnikeddikmktaktflnklyggdmkslvlnfakneelnnkeieelrdil 116 d1on2a1 62 ------ 62 d1sd4a_ 117 ndiskk 122 FAST alignment (Normalized score: 5.84 Raw score:504.10) d1on2a1 1 ---TTPSMEMYIEQIYMLIEEKGYARVSDIAEA----LAVHPSSVTKMVQKLDKDEYLIY 53 :::::::::::::: :::::::::::: ::::::::::::::::::::::: d1sd4a_ 1 QVEISMAEWDVMNIIWD----KKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKR 56 d1on2a1 54 EKYRGLVL---------------------------------------------------- 61 : d1sd4a_ 57 Y-------KSENIYFYSSNIKEDDIKMKTAKTFLNKLYGGDMKSLVLNFAKNEELNNKEI 109 d1on2a1 62 ------------- 62 d1sd4a_ 110 EELRDILNDISKK 122 TMalign alignment (TM-score: 0.69 Raw score:41.81) d1on2a1 1 ---TTPSMEMYIEQIYMLIEEKGYARVSDIAEALA-----VHPSSVTKMVQKLDKDEYLI 52 :::::::::::::: : ::::::::::::: :: ::::::::::::::::: d1sd4a_ 1 QVEISMAEWDVMNIIWD-K---KSVSANEIVVEIQKYKEVSD-KTIRTLITRLYKKEIIK 55 d1on2a1 53 YEKY---RGLVL------------------------------------------------ 61 :::: ::::: d1sd4a_ 56 RYKSENIYFYSSNIKEDDIKMKTAKTFLNKLYGGDMKSLVLNFAKNEELNNKEIEELRDI 115 d1on2a1 62 ------- 62 d1sd4a_ 116 LNDISKK 122 HHsearch alignment (Probability: 0.98 E-value:0.00) d1on2a1 13 YMLIEEKGYARVSDIAEALA----VHPSSVTKMVQKLDKDEYLIYEKYRG 58 :::::::::::::::::::: :::::::::::::::::::::::::: d1sd4a_ 12 MNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSEN 61