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: T0611_Ad2.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.664 --> Intermediate <-- 0.665 --> Hit

SVM
score
SVM
score

The query (T0611_Ad2.pdb) is transitively linked to the hit (d1cuna2) through the intermediate protein (d1m62a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1m62a_ Silencer of death domains,​ Sodd (Bag4)BAG domainSpectrin repeat-​likeAll α
Hit d1cuna2 Spectrin alpha chainSpectrin repeatSpectrin repeat-​likeAll α

Supporting Alignments

Query <-- 0.664 --> Intermediate
DALI alignment (Z-score: 5.5 Raw score:256.50) query 1 ------------FQEYEKLVDYYL-DIPEdRPIT--LEDMTFYLESVFDGLWSyrffhrd 45 :::::::::::: :::: :::: ::::::::::::::::: d1m62a_ 1 gspeftppsikkIIHVLEKVQYLEqEVEE-FVGKktDKAYWLLEEMLTKELLE----lds 55 query 46 LEYLldSDPRLRQDYREFTNRCLAAINRIFAKLAdagiiqpqpedlrsamslnvwlvitn 105 :::: :::::::::::::::::::::::::::: d1m62a_ 56 VETG--GQDSVRQARKEAVCKIQAILEKLEKKGL-------------------------- 87 query 106 wmaflktahltelkqgiyqvltlevpyltpeyrervlalrekyrp 150 d1m62a_ 88 --------------------------------------------- 88 FAST alignment (Normalized score: 3.16 Raw score:360.90) query 1 FQEYEKLVDYYLDIPEDRPI--------TLEDMTFYLESVFDGLWSYRFFHRDLEYLLDS 52 ::::::::::::::::: :::: d1m62a_ 1 --------------------GSPEFTPPSIKKIIHVLEKVQYLEQ----EVEE------- 29 query 53 D------PRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQ--------PEDLRSAMSLN 98 ::::::::::::::::::: ::::::::::: d1m62a_ 30 -FVGKKTDKAYWLLEEMLTKELLELD---------------SVETGGQDSVRQARKEAVC 73 query 99 VWLVITNWMAFLKTAHLTELKQGIYQVLTLEVPYLTPEYRERVLALREKYRP-------- 150 :::::: d1m62a_ 74 KIQAIL----------------------------------------------EKLEKKGL 87 TMalign alignment (TM-score: 0.36 Raw score:54.61) query 1 ------------FQEYEKLVDYYLD-IPEDRPIT---LEDMTFYLESV-FDGLWSYRFFH 43 ::::::::::::: :: :::: ::::::::::: : ::: :: :: d1m62a_ 1 GSPEFTPPSIKKIIHVLEKVQYLEQEVE--EFVGKKTDKAYWLLEEMLTK-ELL-EL-DS 55 query 44 RDLEYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGIIQPQPEDLRSAMSLNVWLVI 103 : :: :::::::::::::::::::::::::::: : d1m62a_ 56 --V-ET-GGQDSVRQARKEAVCKIQAILEKLEKKG----L-------------------- 87 query 104 TNWMAFLKTAHLTELKQGIYQVLTLEVPYLTPEYRERVLALREKYRP 150 d1m62a_ 88 ----------------------------------------------- 88 HHsearch alignment (Probability: 0.01 E-value:0.43) query 42 FHRDLEYLLDSDPRLRQDYREFTNRCLAAINRIFAKLADAGI 83 :::::::::::::::::::::::::::::::::::::::::: d1m62a_ 46 LTKELLELDSVETGGQDSVRQARKEAVCKIQAILEKLEKKGL 87
Intermediate <-- 0.665 --> Hit
DALI alignment (Z-score: 7.3 Raw score:356.60) d1m62a_ 1 gspeftpPSIKKIIHVLEKVQYLEQEVEE-------fvgkkTDKAYWLLEEMLTKELLEL 53 :::::::::::::::::::::: ::::::::::::::::::: d1cuna2 1 -------QFVANVEEEEAWINEKMTLVASedygdtlaaiqgLLKKHEAFETDFTVHKDRV 53 d1m62a_ 54 DS----vETGG------QDSVRQARKEAVCKIQAILEKLEKKGL------- 87 :: :::: ::::::::::::::::::::::::::: d1cuna2 54 NDvcangEDLIkknnhhVENITAKMKGLKGKVSDLEKAAAQRKAkldensa 104 FAST alignment (Normalized score: 8.21 Raw score:780.70) d1m62a_ 1 GSPEFTPP-SIKKIIHVLEKVQYLEQEVEEFVGKKT---------------DKAYWLLEE 44 ::::::::::::::::::: ::::::::: d1cuna2 1 --------QFVANVEEEEAWINEKMTLV--------ASEDYGDTLAAIQGLLKKHEAFET 44 d1m62a_ 45 MLTKELLELDSVETGG---------------QDSVRQARKEAVCKIQAILEKLEKKGL-- 87 ::::::::::: ::::::::::::::::::::::::: d1cuna2 45 DFTVHKDRVND-----VCANGEDLIKKNNHHVENITAKMKGLKGKVSDLEKAAAQR--KA 97 d1m62a_ 88 ------- 88 d1cuna2 98 KLDENSA 104 TMalign alignment (TM-score: 0.64 Raw score:55.49) d1m62a_ 1 -----GSPEFTPPS-IKKIIHVLEKVQYLEQEVEEFVGKKTDKAYWLLEEMLTKELLELD 54 ::: ::::::::::::: ::: :::: : ::::::::::::::::: d1cuna2 1 QFVAN------VEEEEAWINEKMTLVAS--EDY--GDTL--A-AIQGLLKKHEAFETDFT 47 d1m62a_ 55 SV--ET-G-G--------------------QDSVRQARKEAVCKIQAILEKLEKKGL 87 :: :: : : ::::::::::::::::::::::::::: d1cuna2 48 VHKDRVNDVCANGEDLIKKNNHHVENITAKMKGLKGKVSDLEKAAAQRKAKLDENSA 104 HHsearch alignment (Probability: 0.03 E-value:0.94) d1m62a_ 5 FTPPSIKKIIHVLEKVQYLEQEVEEFVGKKTDKAYWLLEEMLTKELLELDSVETGGQDSV 64 ::::::::::::::::::::::::::::: ::::::: :::::::: ::::::: d1cuna2 24 DYGDTLAAIQGLLKKHEAFETDFTVHKDR-----VNDVCAN-GEDLIKKN---NHHVENI 74 d1m62a_ 65 RQARKEAVCKIQAILEKLE 83 ::::::::::::::::::: d1cuna2 75 TAKMKGLKGKVSDLEKAAA 93