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 <-- 1.152 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1k92a1) 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 d1k92a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/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 <-- 1.152 --> Hit
DALI alignment (Z-score: 5.4 Raw score:408.40) d1jfla2 1 ---------fKKAGLLATTGTIvsGVYEKEFSKYGVEIMTPTED---------------- 35 :::::::::::: :::::::::::::::::::: d1k92a1 1 ttilkhlpvgQRIGIAFSGGLD-tSAALLWMRQKGAVPYAYTANlgqpdeedydaiprra 59 d1jfla2 36 ---------EQKD-----------------vmrgiyegvkAGNLKLGRELLLKTAKILEE 69 :::: :::::::::::::::::::: d1k92a1 60 meygaenarLIDCrkqlvaegiaaiqcgafhnttggltyfNTTPLGRAVTGTMLVAAMKE 119 d1jfla2 70 RGAECIIAGCT---evSVVLK---QDDL-KVPLIDPMDVI------------------ae 104 ::::::::::: ::::: :::: ::::::::::: d1k92a1 120 DGVNIWGDGSTykgndIERFYrygLLTNaELQIYKPWLDTdfidelggrhemsefmiacg 179 d1jfla2 105 vavkvalek 113 d1k92a1 180 fdykmsvek 188 FAST alignment (Normalized score: 4.76 Raw score:693.30) d1jfla2 1 ---------FKKAGLLAT-TGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKA 50 ::::::::: :::: :::::::::::::::: d1k92a1 1 TTILKHLPVGQRIGIAFSGGLDT--SAALLWMRQKGAVPYA------------------- 39 d1jfla2 51 ------------------------------------------------------------ 51 d1k92a1 40 YTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYF 99 d1jfla2 51 GNLKLGREL-LLKTAKILEERGAECIIAGC----TEVSVVLKQDD-----LKVPLIDPMD 100 ::::::::: ::::::::::::::::::: :::::: :::: :::::::::: d1k92a1 100 NTTPLGRAVTGTMLVAAMKEDGVNIWGDG-STYKGNDIER-FYRYGLLTNAELQIYKPWL 157 d1jfla2 101 VIAEVAVKVALEK------------------------------- 113 d1k92a1 158 -------------DTDFIDELGGRHEMSEFMIACGFDYKMSVEK 188 TMalign alignment (TM-score: 0.48 Raw score:53.98) d1jfla2 1 -----------------------------------FKKAGLLATT---G-TIVSGVYEKE 21 :::::::::: : ::: : :::: d1k92a1 1 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYD-A-IPRR 58 d1jfla2 22 FSKYGV-EIMTPTEDEQKDVMRGIYE--G--------------VKAGN-LKLGRELLLKT 63 :::::: ::::: : :::: ::: :: : :::: : ::::::::: d1k92a1 59 AMEYGAENARLI-D-CRKQ-LVA-EGIAAIQCGAFHNTTGGLT-YFNTTP-LGRAVTGTM 112 d1jfla2 64 AKILEERG-A-ECIIA-----GCTEVSV--VLKQDDL-----KVPLID---------PMD 100 :::::::: : ::::: :: ::::::: :::::: d1k92a1 113 LVAAMKEDGVNIWGDGSTYKG-----NDIERFYRYGLLTNAELQIYKPWLDTDFIDE--- 164 d1jfla2 101 VIAEVAVKV-----------------ALEK 113 ::::: :: d1k92a1 165 -LGGRH-EMSEFMIACGFDYKMSVEK---- 188 HHsearch alignment (Probability: 0.04 E-value:0.09) d1jfla2 60 LLKTAKILEERGAECIIAGCT-------EVSVVLKQDDLKVPLIDPMDVI--------AE 104 ::::::::::::::::::::: :::::::::::::::::::::: :: d1k92a1 110 GTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRH 169 d1jfla2 105 VAVKVALE 112 :::::::: d1k92a1 170 EMSEFMIA 177