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 <-- 0.758 --> Hit

SVM
score
SVM
score

The query (T0611_Ad2.pdb) is transitively linked to the hit (d1lkia_) 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 d1lkia_ Leukemia inhibitory factor (LIF)4-​helical cytokines4-​helical cytokinesAll 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 <-- 0.758 --> Hit
DALI alignment (Z-score: 3.0 Raw score:231.00) d1m62a_ 1 -------------------gspeftppsiKKII--------------hvlekvqyleqev 27 :::: d1lkia_ 1 natcairhpchgnlmnqiknqlaqlngsaNALFisyytaqgepfpnnveklcapnmtdfp 60 d1m62a_ 28 eefvgkkTDKAYWLLEEMLTKELLELDS--VETG----GQDSVRQARKEAVCKIQAILEK 81 ::::::::::::::::::::: :::: :::::::::::::::::::::: d1lkia_ 61 sfhgngtEKTKLVELYRMVAYLSASLTNitRDQKvlnpTAVSLQVKLNATIDVMRGLLSN 120 d1m62a_ 82 LEKKGL---------------------------------------------- 87 :::::: d1lkia_ 121 VLCRLCnkyrvghvdvppvpdhsdkeafqrkklgcqllgtykqvisvvvqaf 172 FAST alignment (Normalized score: 2.99 Raw score:365.80) d1m62a_ 1 GSPEFT-----------PPSIKKIIHVLEKVQYLEQEVEEFVG----------------- 32 ::::::::::::::::::::::: d1lkia_ 1 ------NATCAIRHPCHGNLMNQIKNQLAQLNGSANALFI---SYYTAQGEPFPNNVEKL 51 d1m62a_ 33 ---------------------------------------------KKTDKAYWLLEEMLT 47 ::::::::::::::: d1lkia_ 52 CAPNMTDFPSFHGNGTEKTKLVELYRMVAYLSASLTNITRDQKVLNPTAVSLQVKLNATI 111 d1m62a_ 48 KELLELDSVETGGQDSVRQARKEAVCKIQAILEKLEKKGL-------------------- 87 ::::::: d1lkia_ 112 DVMRGLL---------------------------------SNVLCRLCNKYRVGHVDVPP 138 d1m62a_ 88 ---------------------------------- 88 d1lkia_ 139 VPDHSDKEAFQRKKLGCQLLGTYKQVISVVVQAF 172 TMalign alignment (TM-score: 0.50 Raw score:43.90) d1m62a_ 1 ---------------------------------GSPEFTPPSI------K--K------- 12 ::::: : : d1lkia_ 1 NATCAIRHPCHGNLMNQIKNQLAQLNGSANALF-----ISYYTAQGEPFPNNVEKLCAPN 55 d1m62a_ 13 ------IIHVLEKVQYL-EQE--VEEFVGKKTD-KAYWLLEEMLTKELLELDSV--ET-- 58 : : ::: : :: :::::::::::::::: :: d1lkia_ 56 MTDFPS----------FH--GNG---TEK---TK-LV-ELYRMVAYLSASLTNITRDQKV 95 d1m62a_ 59 --GGQDSVRQARKEAVCKIQAILEKLEKKGL----------------------------- 87 ::::::::::::::::::::::::::::: d1lkia_ 96 LNPTAVSLQVKLNATIDVMRGLLSNVLCRLCNKYRVGHVDVPPVPDHSDKEAFQRKKLGC 155 d1m62a_ 88 ----------------- 88 d1lkia_ 156 QLLGTYKQVISVVVQAF 172 HHsearch alignment (Probability: 0.00 E-value:1.70) d1m62a_ 31 VG 32 :: d1lkia_ 86 LT 87