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 | d1gcaa_ | Galactose/glucose-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 <-- 0.877 --> HitDALI alignment (Z-score: 5.6 Raw score:401.30) d1jfla2 1 -fKKAGLLA-TTGT----ivsGVYEKEFSKY-GVEIMTPtedeqkdVMRGIyegvkagnl 53 ::::::: :::: :::::::::: ::::::: ::::: d1gcaa_ 1 adTRIGVTIyKYDDnfmsvvrKAIEKDGKSApDVQLLMN------dSQNDQ--------- 45 d1jfla2 54 klgrELLLKTAKILEERGAECIIAGCTEvSVVL--KQDDL---KVPLIDPM--------- 99 :::::::::::::::::::::::: :::: ::::: :::::::: d1gcaa_ 46 ----SKQNDQIDVLLAKGVKALAINLVD-PAAAgtVIEKArgqNVPVVFFNkepsrkald 100 d1jfla2 100 ------DVIA-------------------------------------------------- 103 :::: d1gcaa_ 101 sydkayYVGTdskesgviqgdliakhwqanqgwdlnkdgkiqyvllkgepghpdaeartt 160 d1jfla2 104 ------------------------------------------------------------ 104 d1gcaa_ 161 yvvkelndkgiqteqlaldtamwdtaqakdkmdawlsgpnankievvianndamamgave 220 d1jfla2 104 ------------------------------------------------------------ 104 d1gcaa_ 221 alkahnkssipvfgvdalpealalvksgamagtvlndannqakatfdlaknlaegkgaad 280 d1jfla2 104 ----------EVAVkvALEK----------- 113 :::: :::: d1gcaa_ 281 gtswkienkiVRVP--YVGVdkdnlseftqk 309 FAST alignment (Normalized score: 2.47 Raw score:462.20) d1jfla2 1 ------------------------------------------------------------ 1 d1gcaa_ 1 ADTRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGV 60 d1jfla2 1 ------------------------------------------------------------ 1 d1gcaa_ 61 KALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQG 120 d1jfla2 1 -------------------FKKAGLLA-------TTGTIVSGVYEKEFSK--YGVEIMTP 32 :::::::: ::::: ::::::::: ::::: d1gcaa_ 121 DLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEART--TYVVKELNDKGIQTEQ--- 175 d1jfla2 33 TEDEQKDVMRGIYEGVKAG--------NLKLGRELLLKTAKILE----ERGAECIIAGCT 80 ::::::::::::: :::::::::::: d1gcaa_ 176 -------------------LALDTAMWDTAQAKDKMDAWL----SGPNANKIEVVIANND 212 d1jfla2 81 EVSVVLKQDD----------LKVPLIDPMDVIAEVAVKVALEK----------------- 113 ::::: :::::::: d1gcaa_ 213 AMAMG-----AVEALKAHNKSSIPVFGV---------------DALPEALALVKSGAMAG 252 d1jfla2 114 --------------------------------------------------------- 114 d1gcaa_ 253 TVLNDANNQAKATFDLAKNLAEGKGAADGTSWKIENKIVRVPYVGVDKDNLSEFTQK 309 TMalign alignment (TM-score: 0.55 Raw score:62.49) d1jfla2 1 ------------------------------------------------------------ 1 d1gcaa_ 1 ADTRIGVTIYKYDDNFMSVVRKAIEKDGKSAPDVQLLMNDSQNDQSKQNDQIDVLLAKGV 60 d1jfla2 1 ------------------------------------------------------------ 1 d1gcaa_ 61 KALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGVIQG 120 d1jfla2 1 -------------F-----K-KAGLLAT-T-G-TIVS--GVYEKEFSKY-GVEIM-TPTE 34 : : ::::::: : : :::: :::::::::: ::::: :: d1gcaa_ 121 DLIAKHWQANQGWDLNKDGKIQYVLLKGEPGHPDAEARTTYVVKELNDKGIQTEQLAL-- 178 d1jfla2 35 DEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEER-GAECIIAGCTEVSVVLK--QD-D 90 :: :: :: : : :::::::: ::::::: ::::::::::::::::: :: : d1gcaa_ 179 --DT-AM--WD--T----A-QAKDKMDA-WLSGPNANKIEVVIANNDAMAMGAVEALKAH 225 d1jfla2 91 -LKVPLIDPM---------D------V--------------------------------- 101 ::::::::: : : d1gcaa_ 226 NKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKNLAEGKGAADGTSWK 285 d1jfla2 102 ------------IAEVAVKVA----LEK 113 ::::::: : d1gcaa_ 286 IENKIVRVPYVGVDKDNLS-EFTQK--- 309 HHsearch alignment (Probability: 0.10 E-value:0.02) d1jfla2 60 LLKTAKILEERGA-ECIIAGCTEVSVVLKQDDLK---VPLIDPMDVIAEVAVKVAL 111 ::::::::::::: :::::::::::::::::::: ::::::::::::::::::: d1gcaa_ 215 AMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAK 270