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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.802 --> Intermediate <-- 1.208 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1nqua_) through the intermediate protein (d1jfla2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jfla2 Aspartate racemaseAspartate/​glutamate racemaseATC-​likeα/β
Hit d1nqua_ Lumazine synthaseLumazine synthaseLumazine synthaseα/β

Supporting Alignments

Query <-- 0.802 --> Intermediate
DALI alignment (Z-score: 1.0 Raw score:191.90) query 1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE 23 ::::::: :::: ::::::::: d1jfla2 1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE 58 query 24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg 82 ::::::::::::::::::: :::: :::: d1jfla2 59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l 91 query 83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv 142 ::::: d1jfla2 92 KVPLI------------------------------------------------------- 96 query 143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel 202 d1jfla2 97 ------------------------------------------------------------ 97 query 203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa 262 d1jfla2 97 ------------------------------------------------------------ 97 query 263 eaepptgvvddglridrlviseeplpayeaelaggyadrl 302 d1jfla2 97 -----------------------dpmdviaevavkvalek 113 FAST alignment (Normalized score: 1.26 Raw score:232.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAI---------------LRWTRHSAEQGAHLVAFPEM 45 :::::::::::: d1jfla2 1 -------------------------FKKAGLLATTGTIVSGVYEKEFSKYGV-------- 27 query 46 ALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPA 105 d1jfla2 28 ------------------------------------------------------------ 28 query 106 GAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDL 165 d1jfla2 28 ------------------------------------------------------------ 28 query 166 WQDG----------------------------------GRVPAARSAGAGLLLSVNASPY 191 :::::::::::::::: d1jfla2 28 ----EIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIA------ 77 query 192 ERDKD--DTRLELVRK-RAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQF 248 :::::: ::::::::::: d1jfla2 78 -----GCTEVSVV---LKQDDLKVPLID-------------------------------- 97 query 249 SEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL------ 302 d1jfla2 98 ------------------------------------------------------PMDVIA 103 query 303 ---------- 303 d1jfla2 104 EVAVKVALEK 113 TMalign alignment (TM-score: 0.20 Raw score:60.72) query 1 -SLQLR-LA-LN-QIDSTV-GDIAGN--AEAI--LRWT-RHSAEQGAHLV-AF-----PE 44 : : : :::: : : :: :: :::::: : d1jfla2 1 F----KK-AG-LL--ATTGT-----IVS---GVY--EKE-FS--KYGVEIM-TPTEDE-- 36 query 45 MA-LTG-YPV---EDLALRSSFVEASRTALRELAARLAEEGFGELPVLVG-Y--LDRSES 96 : ::: ::: :: :::::::::::::::::::: : : ::::: : :: d1jfla2 37 -QKDVMRGIYEGVKA-GNLKLGRELLLKTAKILEER-G----A--ECIIAGCTEVS---- 83 query 97 AQPKYGQPAGAPRNAAA--VLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHG 154 ::::: :::::::: d1jfla2 84 ------------VVLKQDD-----LKVPLIDP---------------------------- 98 query 155 VDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTT 214 :::: : : : : :::::: d1jfla2 99 ----MDVI--A------E----------V-------------------A--VKVALE--- 112 query 215 AYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDG 274 : d1jfla2 113 -----------------------K------------------------------------ 113 query 275 LRIDRLVISEEPLPAYEAELAGGYADRL 302 d1jfla2 114 ---------------------------- 114 HHsearch alignment (Probability: 0.06 E-value:0.03) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.208 --> Hit
DALI alignment (Z-score: 4.0 Raw score:308.90) d1jfla2 1 -----------fKKAGLLA-------TTGTIvsGVYEKEFSKYGV---EIMTPtedeqkd 39 ::::::: ::::: :::::::::::: ::::: d1nqua_ 1 mqiyegkltaegLRFGIVAsrfnhalVDRLV--EGAIDCIVRHGGreeDITLV------r 52 d1jfla2 40 VMRGIyegvkagnlklgreLLLKTAKILEER-GAECIIAGC-------------tevSVV 85 ::::: :::::::::::: ::::::::: ::: d1nqua_ 53 VPGSW--------------EIPVAAGELARKeDIDAVIAIGvlirgatphfdyiaseVSK 98 d1jfla2 86 LKQDDL---KVPLIDP-------------------------mdviaevavkvalek 113 :::::: ::::::: d1nqua_ 99 GLANLSlelRKPITFGvitadtleqaieragtkhgnkgweaalsaiemanlfkslr 154 FAST alignment (Normalized score: 4.52 Raw score:596.20) d1jfla2 1 -----------FKKAGLLA-------TTGTIVSGVYEKEFSKYGV---EIMTPTEDEQKD 39 :::::::: ::::: :::::::::::: :::: d1nqua_ 1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLV--EGAIDCIVRHGGREEDITL-------- 50 d1jfla2 40 VMRGIYEGVKAGNLKLG-----RELLLKTAKILEE-RGAECIIAG--------------- 78 ::::::::::::: :::::::: d1nqua_ 51 -----------------VRVPGSWEIPVAAGELARKEDIDAVIA-IGVLIRGATPHFDYI 92 d1jfla2 79 CTEVSVVL---KQDDLKVPLIDPMDVIAEVAVKVALEK---------------------- 113 ::::::: ::::::::::: d1nqua_ 93 ASEVSKG-LANLSLELRKPITF----------------GVITADTLEQAIERAGTKHGNK 135 d1jfla2 114 ------------------- 114 d1nqua_ 136 GWEAALSAIEMANLFKSLR 154 TMalign alignment (TM-score: 0.52 Raw score:58.28) d1jfla2 1 ---------F--KKAGLLATT--G---TIVSGVYEKEFSKYGV---EIMTPTEDEQKDVM 41 : ::::::::: : :::::::::::::::: ::::: : :: d1nqua_ 1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLV----R--VP 54 d1jfla2 42 RGIYEGVKAGNLKLGRELLLKTAKILEER-GAECIIAGCT------------E-VSVVLK 87 : : : :::::::::::: :::::::::: : :::::: d1nqua_ 55 G-S-----------W--EIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGL 100 d1jfla2 88 QDDL--K-VPLIDP--------------------M--DVI---------------AEVAV 107 :::: : :::::: : :: d1nqua_ 101 ANLSLELRKPITFGVITADTLEQAIERAGTKHGNKGW-EAALSAIEMANLFKSLR----- 154 d1jfla2 108 KVALEK 113 d1nqua_ 155 ------ 155 HHsearch alignment (Probability: 0.02 E-value:0.19) d1jfla2 55 LGRELLLKTAKILEERGAECI-IAGC 79 ::::::::::::::::::::: :::: d1nqua_ 55 GSWEIPVAAGELARKEDIDAVIAIGV 80