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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1uf5a_ | N-carbamoyl-D-aminoacid amidohydrolase | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase | α+β |
| Hit | d1b74a1 | Glutamate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
Query <-- 1.647 --> IntermediateDALI alignment (Z-score: 24.9 Raw score:2592.30) query 1 SLQLRLALNQIDSTV--GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALtGYPVE----- 53 ::::::::::::::: :::::::::::::::::::::::::::::::: ::::: d1uf5a_ 1 TRQMILAVGQQGPIAraETREQVVVRLLDMLTKAASRGANFIVFPELAL-TTFFPrwhft 59 query 54 --dLALRssFVEASRT-ALRELAARLAeegFGELPVLVGYLDRSESAqpkygqPAGAPRN 110 :::: ::::::: :::::::::: ::::::::::::::::: ::::::: d1uf5a_ 60 deaELDS-fYETEMPGpVVRPLFEKAA---ELGIGFNLGYAELVVEG------GVKRRFN 109 query 111 AAAVLH-RGRVALTFAKHHLPNY--------gVFDEFRYFVPGD-TMPIVRLHGVDIALA 160 :::::: :::::::::::::::: :::::::::::: ::::::::::::::: d1uf5a_ 110 TSILVDkSGKIVGKYRKIHLPGHkeyeayrpfQHLEKRYFEPGDlGFPVYDVDAAKMGMF 169 query 161 ICEDLWQDgGRVPAARSAGAGLLLSVNASPYE------RDKD--DTRLELVRKRAQEAGC 212 :::::::: ::::::::::::::::::::::: :::: :::::::::::::::: d1uf5a_ 170 IANDRRWP-EAWRVMGLRGAEIICGGYNTPTHnppvpqHDHLtsFHHLLSMQAGSYQNGA 228 query 213 TTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPaaeaepptgvvd 272 :::::::::::::::::::::::::::::::::::::::::::::::: d1uf5a_ 229 WSAAAGKAGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLD------------ 276 query 273 dglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvakngfrsvligl 332 d1uf5a_ 277 ------------------------------------------------------------ 277 query 333 sggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtglnfrtvsiepmf 392 d1uf5a_ 277 ------------------------------------------------------------ 277 query 393 daymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgystlygdsvga 452 d1uf5a_ 277 ------------------------------------------------------------ 277 query 453 ygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgad 512 d1uf5a_ 277 ------------------------------------------------------------ 277 query 513 aivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1uf5a_ 277 -----------------------------rcrelrehifnfkqhrqpqhygliael 303 FAST alignment (Normalized score: 13.16 Raw score:5458.00) query 1 SLQLRLALNQ-IDSTVG-DIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL- 57 :::::::::: :::::: ::::::::::::::::::::::::::::::::: d1uf5a_ 1 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTT--------F 52 query 58 -----------RSSFVEAS------RTALRELAARLAEEGFGELPVLVGYLDRSESAQPK 100 :::: ::::::::::::: ::::::::::::: d1uf5a_ 53 FPRWHFTDEAELDSF----YETEMPGPVVRPLFEKAAE---LGIGFNLGYAELV------ 99 query 101 YGQP----AGAPRNAAAV-LHRGRVALTFAKHHLPNYG------------VFDEFRYFVP 143 :::::::::: ::::::::::::::: :::::::::: d1uf5a_ 100 ----VEGGVKRRFNTSILVDKSGKIVGKYRKIHL----PGHKEYEAYRPFQHLEKRYFEP 151 query 144 GD-TMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKD------ 196 :: ::::::::::::::::::::::: ::::::::::::::::::::: d1uf5a_ 152 GDLGFPVYDVDAAKMGMFIANDRRWP-EAWRVMGLRGAEIICGGYNTP------THNPPV 204 query 197 --------DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQF 248 :::::::::::::::::::::::::::::::::::::::::::::::::::: d1uf5a_ 205 PQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKAGMEENCMLLGHSCIVAPTGEIVALTTTL 264 query 249 SEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEV 308 :::::::::: d1uf5a_ 265 EDEVITAAVD-------------------------------------------------- 274 query 309 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 368 d1uf5a_ 275 ------------------------------------------------------------ 275 query 369 KGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHI 428 d1uf5a_ 275 ------------------------------------------------------------ 275 query 429 VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEAS 488 d1uf5a_ 275 ------------------------------------------------------------ 275 query 489 ITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKIS 548 d1uf5a_ 275 ------------------------------------------------------------ 275 query 549 AKGFGKDRRLPITNRWREGH----------------------------- 568 d1uf5a_ 275 --------------------LDRCRELREHIFNFKQHRQPQHYGLIAEL 303 TMalign alignment (TM-score: 0.41 Raw score:233.10) query 1 SLQLRLALNQID-STVGD-IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV-E-DLA 56 :::::::::::: ::::: ::::::::::::::::::::::::::::::::::: : ::: d1uf5a_ 1 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTD 60 query 57 LR-SSFVEASRTALRELAARLAEEGFG-ELPVLVGYLDRSESAQPKYGQPAGAPRNAAAV 114 :: ::::: :::::::::::::::::: ::::::::::::::: ::::::::::: d1uf5a_ 61 EAELDSFY-ETEMPGPVVRPLFEKAAELGIGFNLGYAELVVEG------GVKRRFNTSIL 113 query 115 LH-RGRVALTFAKHHLPNYG--------VFDEFRYFVPGDT-MPIVRLHGVDIALAICED 164 :: ::::::::::::::::: ::::::::::::: :::::::::::::::::: d1uf5a_ 114 VDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFIAND 173 query 165 LWQDGGRVPAARSAGAGLLLSVNASPYE-------RDKD-DTRLELVRKRAQEAGCTTAY 216 ::::: :::::::::::::::::::::: :::: :::::::::::::::::::: d1uf5a_ 174 RRWPE-AWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAA 232 query 217 LAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAE------------- 263 ::::::::::::::::::::::::::::::::::::::::::::::: d1uf5a_ 233 AGKAGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQHR 292 query 264 -------AEPPTGVVDDG-LRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVG 315 ::: d1uf5a_ 293 QPQHYGL--------IAEL----------------------------------------- 303 query 316 LRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAEL 375 d1uf5a_ 304 ------------------------------------------------------------ 304 query 376 ARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNK 435 d1uf5a_ 304 ------------------------------------------------------------ 304 query 436 SELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYP 495 d1uf5a_ 304 ------------------------------------------------------------ 304 query 496 VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD 555 d1uf5a_ 304 ------------------------------------------------------------ 304 query 556 RRLPITNRWREGH 568 d1uf5a_ 304 ------------- 304 HHsearch alignment (Probability: 1.00 E-value:0.00) query 1 SLQLRLALNQIDST--VGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALR 58 :::::::::::::: :::::::::::::::::::::::::::::::::::::::::::: d1uf5a_ 1 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTD 60 query 59 SSFVEASRT------ALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAA 112 ::::::::: :::::::::::: :::::::::::::: :::::::::: d1uf5a_ 61 EAELDSFYETEMPGPVVRPLFEKAAEL---GIGFNLGYAELVVE------GGVKRRFNTS 111 query 113 AVLHR-GRVALTFAKHHLPNYGVFD--------EFRYFVPGDT-MPIVRLHGVDIALAIC 162 ::::: ::::::::::::::::::: :::::::::: :::::::::::::::: d1uf5a_ 112 ILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFIA 171 query 163 EDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDT--------RLELVRKRAQEAGCTT 214 ::::::: :::::::::::::::::::::::::::: :::::::::::::::: d1uf5a_ 172 NDRRWPE-AWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWS 230 query 215 AYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDG 274 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1uf5a_ 231 AAAGKAGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQ 290 query 275 LRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALV 313 :::: ::::::: d1uf5a_ 291 HRQP----------------------------QHYGLIA 301
Intermediate <-- 1.431 --> HitDALI alignment (Z-score: 2.5 Raw score:295.60) d1uf5a_ 1 trqMILAVGQQG----------------------------PIARaETREQVVVRLLDMLT 32 ::::::::: :::: ::::::::::::::: d1b74a1 1 ---MKIGIFDSGvggltvlkairnryrkvdivylgdtarvPYGI-RSKDTIIRYSLECAG 56 d1uf5a_ 33 KAASRGANFIVFPELALttffprwhftdeaeldsfyetempgpvvRPLFEKAAelgIGFN 92 ::::::::::::::::: :::::::: :::: d1b74a1 57 FLKDKGVDIIVVACNTA-----------------------sayalERLKKEIN---VPVF 90 d1uf5a_ 93 LGYaelvveggvkrrfntsilvdksgkivgKYRKIhlpghkeyeayrpfqhlekryfepG 152 ::: ::::: : d1b74a1 91 GVI--------------------------ePGVKE------------------------A 100 d1uf5a_ 153 DLGfpvydvdaakmgmfiandrrwpeawrvmglrgaeiicggyntpthnppvpqhdhlts 212 ::: d1b74a1 101 LKK--------------------------------------------------------- 103 d1uf5a_ 213 fhhllsmqagsyqngawsaaagkagmeencmllghscivaptgeivaltttledevitaa 272 d1b74a1 104 ------------------------------------------------------------ 104 d1uf5a_ 273 vdldrcrelrehifnfkqhrqpqhygliael 303 d1b74a1 104 -----------------------------sr 105 FAST alignment (Normalized score: 2.61 Raw score:464.80) d1uf5a_ 1 TRQMILAVGQQGPI-------------------------------ARAETREQVVVRLLD 29 ::::::: ::::::::::::::: d1b74a1 1 ---MKIGIFD----SGVGGLTVLKAIRNRYRKVDIVYLGDTARVPYGIRSKDTIIRYSLE 53 d1uf5a_ 30 MLTKAASRGANFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPV----------VRP 79 :::::::::::::: ::: d1b74a1 54 CAGFLKDKGVDIIV---------------------------------VACNTASAYALER 80 d1uf5a_ 80 LFEKAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYR 139 :::: ::::::: d1b74a1 81 LKKE---INVPVFG---------------------------------------------- 91 d1uf5a_ 140 PFQHLEKRYFEPGDLGFPVYDVDAAKMGMFIANDRRWPEAWRVMGLRGAEIICGGYNTPT 199 d1b74a1 92 ------------------------------------------------------------ 92 d1uf5a_ 200 HNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKAGMEENCMLLGHSCIVAPTGEIVA 259 d1b74a1 92 ------------------------------------------------------------ 92 d1uf5a_ 260 LTTTLEDEVITAAVDLDRCRELREHIFNFKQHRQPQHYGLIAEL-------------- 303 d1b74a1 92 --------------------------------------------VIEPGVKEALKKSR 105 TMalign alignment (TM-score: 0.21 Raw score:64.50) d1uf5a_ 1 TR---QMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWH 57 : d1b74a1 1 -MKIG------------------------------------------------------- 4 d1uf5a_ 58 FTDEAELDSFYETEMPGPVVRPLFEKAAELGIGFN-LG-YAELVVEGGVKRRFNT-S--I 112 : : ::: : : d1b74a1 5 ----------------------------------IF-DS-------------GVGGLTVL 16 d1uf5a_ 113 --LV-DKSGKIVGKYRKI--HLPGHKEYEAYRPFQH-----LEKRYFEPGDLGFPVYDVD 162 :: ::: ::::::::: ::::: : d1b74a1 17 KAIRNRYR-KVDIVYLGDTARVPYG----------IRSKDT------------------- 46 d1uf5a_ 163 AAKMGMFIANDRR-W-PEAWRVMGLRGAEIICGGYNT-PTHNPPVPQHDHLTSFHHLLSM 219 :: : ::::::::::::::::::::: ::: :: d1b74a1 47 -----------IIRYSLECAGFLKDKGVDIIVVACNTA----------------SAY-AL 78 d1uf5a_ 220 QAGSYQNGAWSAAAGKAGMEENCMLLGHSCIVAPTGEIVALTTTLEDEV--ITAAVDLDR 277 :::::::::::::: ::: :::: :::: d1b74a1 79 ERLKKEINVPVFGV--------------IEP---------GVKE-ALKKSR--------- 105 d1uf5a_ 278 CRELREHIFNFKQHRQPQHYGLIAEL 303 d1b74a1 106 -------------------------- 106 HHsearch alignment (Probability: 0.16 E-value:0.02) d1uf5a_ 178 EAWRVMGLRGAEIICGGYNTP 198 ::::::::::::::::::::: d1b74a1 53 ECAGFLKDKGVDIIVVACNTA 73