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 | d1jyea_ | Lac-repressor (lacR) core (C-terminal domain) | 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 <-- 1.667 --> HitDALI alignment (Z-score: 7.5 Raw score:445.70) d1jfla2 1 fKKAGLLATTG----TIVS-GVYEKEFSKYGVEIMTPtedeqkdVMRGiyegvkagnlkl 55 :::::::::: :::: ::::::::::::::::: :::: d1jyea_ 1 -LLIGVATSSLalhaPSQIvAAILSRADQLGASVVVS------mVERS------------ 41 d1jfla2 56 GRELLLKTAKILEERGAECIIAGCTE---vSVVLKqDDLK-VPLIDP---------MDVI 102 :::::::::::::::::::::::::: ::::: :::: :::::: :::: d1jyea_ 42 GVEACKTAVHNLLAQRVSGLIINYPLddqdAIAVE-AACTnVPALFLdvsdqtpinSIIF 100 d1jfla2 103 ------------------------------------------------------------ 103 d1jyea_ 101 shedgtrlgvehlvalghqqiallagplssvsarlrlagwhkyltrnqiqpiaeregdws 160 d1jfla2 103 ------------------------------------------------------------ 103 d1jyea_ 161 amsgfqqtmqmlnegivptamlvandqmalgamraitesglrvgadisvvgyddtedssc 220 d1jfla2 103 -----------------------------------AEVA-----vkvalek 113 :::: d1jyea_ 221 yipplttikqdfrllgqtsvdrllqlsqgqavkgnQLLPvslvkrkttlap 271 FAST alignment (Normalized score: 3.25 Raw score:568.60) d1jfla2 1 F----------------------------------------------------------- 1 d1jyea_ 1 -LLIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVS 59 d1jfla2 2 -----------------------------------------------------------K 2 : d1jyea_ 60 GLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQ 119 d1jfla2 3 KAGLLA-------TTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKL 55 :::::: ::::: :::::::::::::: d1jyea_ 120 QIALLAGPLSSVSARLRL--AGWHKYLTRNQIQP-------------------------- 151 d1jfla2 56 --------GRELLLKTAKILEE--RGAECIIAGCTEVSVVLKQDDL-------------- 91 :::::::::::::: :::::::::::::::: d1jyea_ 152 IAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALG------AMRAITESGLRVGA 205 d1jfla2 92 KVPLIDPMDVIAEVAVKVALEK-------------------------------------- 113 ::::::: d1jyea_ 206 DISVVGY---------------DDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQ 250 d1jfla2 114 --------------------- 114 d1jyea_ 251 AVKGNQLLPVSLVKRKTTLAP 271 TMalign alignment (TM-score: 0.54 Raw score:61.47) d1jfla2 1 ------------------------------------------------------------ 1 d1jyea_ 1 LLIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSG 60 d1jfla2 1 ---------------------------------------------------------FKK 3 ::: d1jyea_ 61 LIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQ 120 d1jfla2 4 AGLLATTG----TIV-SGVYEKEFSKYGVEI-MTPTEDEQKDVMRGIYEGVKAGNLKLG- 56 :::::::: ::: ::::::::::::::: ::: : :: : : : : d1jyea_ 121 IALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAER----E--GD--W---S----A--MS 163 d1jfla2 57 RELLLKTAKILEERGAECIIAGCTEVSVVLKQ-DD---L----KVPLIDPM--------- 99 ::::::::::: :::::::::::::::::::: :: : :::::::: d1jyea_ 164 GFQQTMQMLNE-GIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYI 222 d1jfla2 100 ----DV--------------------------------IAEV-------AVKVALEK 113 :: :::: d1jyea_ 223 PPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAP-------- 271 HHsearch alignment (Probability: 0.85 E-value:0.00) d1jfla2 1 FKKAGLLATTGT-----IVSGVYEKEFSKYGVEIMT--PTEDEQKDVMRGIYEGVKAGNL 53 :::::::::::: ::::::::::::::::::: :::::::::::::::::::::: d1jyea_ 118 HQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIV 177 d1jfla2 54 KLG-----RELLLKTAKILEER----GAECIIAGCTEVSVVLKQDDLKVPLID-PMDVIA 103 ::: :::::::::::::: ::::::::::::::::: ::::::::: :::::: d1jyea_ 178 PTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC-YIPPLTTIKQDFRLLG 236 d1jfla2 104 EVAVKVALE 112 ::::::::: d1jyea_ 237 QTSVDRLLQ 245