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 | d1drka_ | D-ribose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 1.461 --> HitDALI alignment (Z-score: 6.1 Raw score:401.50) d1jfla2 1 fKKAGLLA----ttGTIVS-GVYEKEFSKYGVEIMTPtedeqkdVMRGiyegvkagnlkl 55 ::::::: ::::: ::::::::::::::::: :::: d1drka_ 1 kDTIALVVstlnnpFFVSLkDGAQKEADKLGYNLVVL------dSQNN------------ 42 d1jfla2 56 gRELLLKTAKILEERGAECIIAgCTEVSVVLK--QDDL---KVPLIDPM----------D 100 ::::::::::::::::::::: ::::::::: :::: :::::::: : d1drka_ 43 -PAKELANVQDLTVRGTKILLI-NPTDSDAVGnaVKMAnqaNIPVITLDrqatkgevvsH 100 d1jfla2 101 VIA--------------------------------------------------------- 103 ::: d1drka_ 101 IASdnvlggkiagdyiakkagegakvielqgtaatsaarergegfqqavaahkfnvlasq 160 d1jfla2 104 ------------------------------------------------------------ 104 d1drka_ 161 padfdrikglnvmqnlltahpdvqavfaqndemalgalralqtagksdvmvvgfdgtpdg 220 d1jfla2 104 ----------------------------------------EVAVkvALEK--- 113 :::: :::: d1drka_ 221 ekavndgklaatiaqlpdqigakgvetadkvlkgekvqakYPVD--LKLVvkq 271 FAST alignment (Normalized score: 3.74 Raw score:654.70) d1jfla2 1 FKKAGLLA-------TTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNL 53 :::::::: ::::: :::::::::::::::: d1drka_ 1 KDTIALVVSTLNNPFFVSLK--DGAQKEADKLGYNLVV---------------------- 36 d1jfla2 54 KL-----GRELLLKTAKILEERGAECIIAGCTE----VSVVLKQD--------DLKVPLI 96 ::::::::::::::::::::: ::::: ::::::: d1drka_ 37 --LDSQNNPAKELANVQDLTVRGTKILL-----INPTDSDAV---GNAVKMANQANIPVI 86 d1jfla2 97 DPMDVIAE---------------VAVKVALEK---------------------------- 113 :: :::::: d1drka_ 87 TL------DRQATKGEVVSHIASDNVLGG---KIAGDYIAKKAGEGAKVIELQGTAATSA 137 d1jfla2 114 ------------------------------------------------------------ 114 d1drka_ 138 ARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGA 197 d1jfla2 114 ------------------------------------------------------------ 114 d1drka_ 198 LRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKV 257 d1jfla2 114 -------------- 114 d1drka_ 258 QAKYPVDLKLVVKQ 271 TMalign alignment (TM-score: 0.59 Raw score:66.42) d1jfla2 1 FKKAGLLA-TTG----TIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKL 55 :::::::: ::: ::::::::::::::::::::: : :: : : d1drka_ 1 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVL----D--SQ--N--N-------- 42 d1jfla2 56 GRELLLKTAKILEERGAECIIAGCTEVSVVLK--QDDL--K-VPLIDPM----------D 100 : :::::::::::::::::::: ::::::::: :::: : ::::::: : d1drka_ 43 P-AKELANVQDLTVRGTKILLI-NPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSH 100 d1jfla2 101 VIA--------------------------------------------------------- 103 ::: d1drka_ 101 IASDNVLGGKIAGDYIAKKAGEGAKVIELQGTAATSAARERGEGFQQAVAAHKFNVLASQ 160 d1jfla2 104 ------------------------------------------------------------ 104 d1drka_ 161 PADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDG 220 d1jfla2 104 ---------------------------------------EVAV--------KVALEK 113 :::: d1drka_ 221 EKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ------ 271 HHsearch alignment (Probability: 0.16 E-value:0.15) d1jfla2 3 KAGLLATT-----GTIVSGVYEKEFSKYGVEIMTPTED--EQKDVMRGIYEGVKAGNLKL 55 :::::::: ::::::::::::::::::::::::: :::::::::::::::::::: d1drka_ 125 KVIELQGTAATSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQ 184 d1jfla2 56 -----GRELLLKTAKILEERG-AECIIAGCTEVSVVLKQDD--LKVPLID-PMDVIAEVA 106 :::::::::::::::: ::::::::::::::::::: ::::::: ::::::::: d1drka_ 185 AVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKG 244 d1jfla2 107 VKVALE 112 :::::: d1drka_ 245 VETADK 250