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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1bd0a2 | Alanine racemase | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
Query <-- 2.454 --> IntermediateDALI alignment (Z-score: 14.1 Raw score:1260.00) query 1 mietpyylidkAKLTRNMERIAHVReKSGAKALLALKCFA---TWSV-FDLMRD-YMDGT 55 :::::::::::::: :::::::::::::: :::: :::::: ::::: d1bd0a2 1 --------vdlDAIYDNVENLRRLL-PDDTHIMAVVKANAyghGDVQvARTALEaGASRL 51 query 56 TSSSLFEVRLGRE-RFGKETHAYSVAYGDnEIDEVVSHADKIIFNSISQLERFAD---ka 111 ::::::::::::: ::::::::::::::: ::::::::::::::::::::::::: d1bd0a2 52 AVAFLDEALALREkGIEAPILVLGASRPA-DAALAAQQRIALTVFRSDWLEEASAlysgp 110 query 112 aGIARGLRLNPQ--RLGEWDVPKVER-VMDR-------INGFMIHNNceNKDFGL--FDR 159 ::::::::::: :::::::::::: :::: ::::::::: :::::: ::: d1bd0a2 111 fPIHFHLKMDTGmgRLGVKDEEETKRiVALIerhphfvLEGLYTHFA-tADEVNTdyFSY 169 query 160 MLGEIEERFGALiARVDWVSLGG-GIHFtgddypvdaFSARLrafsdrygvQIYLEPGEA 218 :::::::::::: :::::::::: :::: ::::: ::::::::: d1bd0a2 170 QYTRFLHMLEWLpSRPPLVHCANsAASL--------rFPDRT---------FNMVRFGIA 212 query 219 SITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksc 278 :::: d1bd0a2 213 MYGL-------------------------------------------------------- 216 query 279 lagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvref 338 d1bd0a2 217 -----------------------------------------------------apspgik 223 query 339 tyadyeqsls 348 d1bd0a2 224 pllpyplkea 233 FAST alignment (Normalized score: 7.91 Raw score:2253.00) query 1 MIETPYYLIDKA-KLTRNMERIAHVREK--SGAKALLALKCFA---------TWSVFDLM 48 ::::::::::::::: :::::::: :::::::: d1bd0a2 1 ------------VDLDAIYDNVENLRRLLPDDTHIMAV-----VKANAYGHGDVQVARTA 43 query 49 RD-YMDGTTSSSLFEVRLGRE-RFGKETHAYSVAYGDNEIDEVVSHA--DKIIFNSISQL 104 :: :::::::::::::::::: :::::::: :::::::::::::: ::::::::::: d1bd0a2 44 LEAGASRLAVAFLDEALALREKGIEAPILV-LGASRPADAALAAQ--QRIALTVFRSDWL 100 query 105 ERFADKAA----GIARGLRLNP--QRLGEWDVPKVERVMD--------RINGFMIHNNCE 150 ::::::: :::::::::: :::::::::::::::: ::::::: :::: d1bd0a2 101 EEASALY-SGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYT-HFAT 158 query 151 N--KDFGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDA---------F 196 : ::::::::::::::: :::: :::::: : d1bd0a2 159 ADEVNTDYFSYQYTRFLH-MLEW--LPSRPPLVH----------------CANSAASLRF 199 query 197 SARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLL 254 ::: ::::::::: d1bd0a2 200 PDR-----------TFNMVRFGIAM----------------------------------- 213 query 255 IYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNW 314 d1bd0a2 214 ------------------------------------------------------------ 214 query 315 FNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-------------------- 348 d1bd0a2 214 ----------------------------------YGLAPSPGIKPLLPYPLKEA 233 TMalign alignment (TM-score: 0.49 Raw score:170.45) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-F--AT-WSVFDLMRD-YMDGT 55 ::::::::::::::::: :::::::::::: : :: ::::::::: ::::: d1bd0a2 1 --------VDLDAIYDNVENLRRLL-PDDTHIMAVVKANAYGHGDVQVARTALEAGASRL 51 query 56 TSSSLFEVRLGRE-RFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFA-DKAA- 112 ::::::::::::: ::::::::::::::: :::::::::::::::::::::::: :::: d1bd0a2 52 AVAFLDEALALREKGIEAPILVLGASRPA-DAALAAQQRIALTVFRSDWLEEASALYSGP 110 query 113 -GIARGLRLNPQ--RLGEWDVPKVERVMD-RI------N-GFMIHNNCENKDFGL-FDRM 160 ::::::::::: ::::::::::::::: :: : ::::::::::::::: :::: d1bd0a2 111 FPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQ 170 query 161 LGEIEERFGALIARVD-WVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEAS 219 :::::: ::::::::: :::::: :::: :: ::::: : ::::::::: d1bd0a2 171 YTRFLH-MLEWLPSRPPLVHCAN-SAAS---LR---FPDRT---F------NMVRFGIAM 213 query 220 ITKS-------------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNE 266 :::: d1bd0a2 214 YGLAPSPGIKPLLPYPL------------------------------------------- 230 query 267 GSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIR 326 :: : d1bd0a2 231 -----------------------------------KE-A--------------------- 233 query 327 ELDGSVRTVREFTYADYEQSLS 348 d1bd0a2 234 ---------------------- 234 HHsearch alignment (Probability: 0.97 E-value:0.00) query 9 IDKAKLTRNMERIAHVREKSGAKALLALKCFA----TWSVFDLMRDYM-DGTTSSSLFEV 63 :::::::::::::::::: ::::::::::::: :::::::::::: ::::::::::: d1bd0a2 1 VDLDAIYDNVENLRRLLP-DDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEA 59 query 64 RLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAG---IARGLRL 120 :::::::::::::::::::::::::::::::::::::::::::::::::: ::::::: d1bd0a2 60 LALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKM 119 query 121 NPQ--RLGEWDVPKVERVMDRIN--------GFMIHNNCEN-KDFGLFDRMLGEIEERFG 169 ::: :::::::::::::::::: :::::::::: :::::::::::::::::: d1bd0a2 120 DTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLE 179 query 170 ALIARVDWVSLG 181 :::::::::::: d1bd0a2 180 WLPSRPPLVHCA 191
Intermediate <-- 1.561 --> HitDALI alignment (Z-score: 6.6 Raw score:806.80) d1bd0a2 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 d1bd0a2 1 ------------------------------------------------------VDLDAI 6 :::::: d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeKSVPYV 120 d1bd0a2 7 YDNVENLRRLLPDDTHIMAVVKAN-----------------------------------a 31 :::::::::::::::::::::::: d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPftlasyvveggssknftkikrlafaepkvlhallqk 180 d1bd0a2 32 yghGDVQVARTALEAGASRLAVAF---------------lDEALALReKGIE-----API 71 ::::::::::::::::::::: ::::::: :::: ::: d1j93a_ 181 fatSMAKYIRYQADSGAQAVQIFDswatelspvdfeefslPYLKQIV-DSVKlthpnLPL 239 d1bd0a2 72 LVLGASRPADAALAAQQRI-ALTVFRsdWLEEASALysgpfPIHFHLKMDTG-mgrlgvK 129 ::::::::::::::::::: :::::: :::::::: ::::::::::: : d1j93a_ 240 ILYASGSGGLLERLPLTGVdVVSLDWtvDMADGRRR--lgpNVAIQGNVDPGvlfgskeF 297 d1bd0a2 130 DEEETKRIVALIERhphfVLEGLYT--HFATadevntdYFSYqyTRFLHMLEWLPSRppl 187 :::::::::::::: ::::::: :::: :::: ::::::::::::: d1j93a_ 298 ITNRINDTVKKAGK----GKHILNLghGIKV-------GTPE--ENFAHFFEIAKGL--- 341 d1bd0a2 188 vhcansaaslrfpdrtfnmvrfgiamyglapspgikpllpyplkea 233 d1j93a_ 342 --------------------------------------------ry 343 FAST alignment (Normalized score: 3.55 Raw score:1003.00) d1bd0a2 1 V----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 d1bd0a2 2 --------------------------------------------------------DLDA 5 :::: d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 d1bd0a2 6 IYDNVENLRRLLPDDTHIMAVVKANAYGH------------------------------- 34 :::::::::::::::::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV-------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPK 172 d1bd0a2 35 -----------GDVQVARTALEAGASRLAVA----------------FLDEALALREKG- 66 ::::::::::::::::::: :::::::::: d1j93a_ 173 VLHALLQKFATSMAKYIRYQADSGAQAVQI-FDSWATELSPVDFEEFSLPYLKQIVD--S 229 d1bd0a2 67 -----IEAPILVLGASRP-----ADAALAAQQR-IALTVF-------------------- 95 :::::::: :::::::::: ::::: d1j93a_ 230 VKLTHPNLPLILY-----ASGSGGLLERLPLTGVDVVSL-DWTVDMADGRRRLGPNVAIQ 283 d1bd0a2 96 --------------RSDWLEEASALYSGPFP----IHFH--LKMDTGMGRLGV--KDEEE 133 :::::::::::: :::: :::: ::::: d1j93a_ 284 GNVDPGVLFGSKEFITNRINDTVKKA-----GKGKHILNLGHGIK--------VGTPEEN 330 d1bd0a2 134 TKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANS 193 ::::::::::: d1j93a_ 331 FAHFFEIAKGL------------------------------------------------- 341 d1bd0a2 194 AASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEA-- 233 d1j93a_ 342 ----------------------------------------RY 343 TMalign alignment (TM-score: 0.53 Raw score:124.28) d1bd0a2 1 ------------------------------------------------------------ 1 d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1bd0a2 1 -------------------V-------------------------------DLD-AIYDN 9 : ::: ::::: d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 d1bd0a2 10 VENLRRL--LPD-DTHIMAVVKAN-AYG-------------------------------- 33 ::::::: ::: ::::::::::: ::: d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQK 180 d1bd0a2 34 H--GDVQVARTALEAGASRLAVAF--------------LD-EALALREKGI---E-APIL 72 : ::::::::::::::::::::: :: :::::::::: : :::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLI 240 d1bd0a2 73 VLGA-SRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVK-- 129 :::: ::::::::::::::::::::::::::::::::: : ::::::::: : :: d1j93a_ 241 LYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGP-N-VAIQGNVDP--G---VLFG 293 d1bd0a2 130 ---DE-EETKRIVALIERHPHFVLEGLY-THFATADEVNTDYFSYQYTRFLHMLEWL-PS 183 :: :::::::::::: ::::::: ::::: : ::::::::::::: :: d1j93a_ 294 SKEFITNRINDTVKKAGK---GKHILNLGHGIKV-------G--TPEENFAHFFEIAKGL 341 d1bd0a2 184 RPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEA 233 :: d1j93a_ 342 RY------------------------------------------------ 343 HHsearch alignment (Probability: 0.23 E-value:0.09) d1bd0a2 9 NVENLRRLLPDDTHI 23 ::::::::::::::: d1j93a_ 123 ALTILRKEVNNQAAV 137