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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jfla2 | Aspartate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
| Hit | d1eucb1 | Succinyl-CoA synthetase, beta-chain, C-terminal domain | Succinyl-CoA synthetase domains | Flavodoxin-like | α/β |
Query <-- 0.802 --> IntermediateDALI 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 <-- 1.546 --> HitDALI alignment (Z-score: 4.7 Raw score:348.70) d1jfla2 1 -----------------fKKAGLLA-TTGTIvsGVYEKEFSKYGVEIMTptedeqkDVMR 42 ::::::: ::::: :::::::::::::::: :::: d1eucb1 1 epieneaakydlkyigldGNIACFVnGAGLA--MATCDIIFLNGGKPAN----fldLGGG 54 d1jfla2 43 GiyegvkagnlklGRELLLKTAKILEER-GAECIIAGC-------teVSVVL--KQDD-- 90 : ::::::::::::::: ::::::::: ::::: :::: d1eucb1 55 V------------KESQVYQAFKLLTADpKVEAILVNIfggivnxaiIANGItkACREle 102 d1jfla2 91 LKVPLIDP---------------------MDVI--aevavkvalek 113 :::::::: :::: d1eucb1 103 LKVPLVVRlegtnvheaqniltnsglpitSAVDledaakkavasvt 148 FAST alignment (Normalized score: 4.49 Raw score:580.80) d1jfla2 1 F------------------KKAGLLA-TTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVM 41 ::::::: ::::: :::::::::::::: d1eucb1 1 -EPIENEAAKYDLKYIGLDGNIACFVNGAGLA--MATCDIIFLNGGKP------------ 45 d1jfla2 42 RGIYEGVKAGNLKL----------GRELLLKTAKILEE-RGAECIIAG--------CTEV 82 :::::::::::::: :::::::: :::: d1eucb1 46 --------------ANFLDLGGGVKESQVYQAFKLLTADPKVEAILV-NIFGGIVNAAII 90 d1jfla2 83 SVVLKQD--------DLKVPLIDPMDVIAEVAVKVALEK--------------------- 113 ::: :::::::: d1eucb1 91 ANG----ITKACRELELKVPLVV----------------RLEGTNVHEAQNILTNSGLPI 130 d1jfla2 114 ------------------ 114 d1eucb1 131 TSAVDLEDAAKKAVASVT 148 TMalign alignment (TM-score: 0.46 Raw score:52.45) d1jfla2 1 ------------------FKKAGLLATTG-TIVSGVYEKEFSKYGVEIMTPTEDEQK-DV 40 :::::::::: :: ::::::::::::::::::: :: : d1eucb1 1 EPIENEAAKYDLKYIGLD-GNIACFVNGAGLA--MATCDIIFLNGGKPANFLD--LGG-G 54 d1jfla2 41 MRG------------------------IYEGVKAGNLKLGRELLLKTAK-ILEERGAECI 75 ::: :::::: : ::::::::: : :::: ::::: d1eucb1 55 VKESQVYQAFKLLTADPKVEAILVNIFGGIVNA---A-IIANGITKA-CRELEL-KVPLV 108 d1jfla2 76 IAGCTE-VS-VV--LKQDDLKVPLIDPMD-VI---------AEVAVKVALEK 113 :: ::: :: :: ::::::::::::::: :: d1eucb1 109 VR-LEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT----------- 148 HHsearch alignment (Probability: 0.02 E-value:0.41) d1jfla2 52 NLKLGRELLLKTAKILEERGAE---CIIAGCTEVSVVLKQDDL-KVP--LIDPMDVIAEV 105 :::::::::::::::::::::: :::::::::::::::::: ::: ::::::::::: d1eucb1 83 GIVNXAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKK 142 d1jfla2 106 AVKV 109 :::: d1eucb1 143 AVAS 146