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 | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1iv8a2 | Maltooligosyl trehalose synthase | (Trans)glycosidases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 0.740 --> HitDALI alignment (Z-score: 9.4 Raw score:1206.20) d1j93a_ 1 tqpllldavrgkeverpPVWLMRqagrymksyqllcekyplFRDRSenVDLVVEIsLQPW 60 :::::: ::::: ::::::: :::: d1iv8a2 1 ---------------miSATYRL----------------qlNKNFN--FGDVIDN-LWYF 26 d1j93a_ 61 KVFRPDGVILFSdilTPLSgmniPFDIikgkgpvifdplrtaadvekvrEFIP---ekSV 117 :::::::::::: :::: :::: :::: :: d1iv8a2 27 XDLGVSHLYLSP---VLMA----SPGS--------------nhgydvidHSRIndelgGE 65 d1j93a_ 118 PYVGEALTILRKEVnnqAAVLGFVGAPftlaSYVV------------------------- 152 :::::::::::::: :::::::::: :::: d1iv8a2 66 KEYRRLIETAHTIG---LGIIQDIVPN----HMAVnslnwrlmdvlxmgxxsxyytyfdf 118 d1j93a_ 153 ------------------------------------------------------------ 153 d1iv8a2 119 fpeddkirlpilgedldtviskgllkivkdgdeyfleyfkwklpltevgndiydtlqkqn 178 d1j93a_ 153 ----------eggSSKNFTKikrlafaepkvLHALLQKFATsmaKYIRYQadsgAQAVQI 202 ::::::: :::::::::: :::::: :::::: d1iv8a2 179 ytlmswknppsyrRFFDVNT----ligvnveXDHVFQESHS---XILDLD----VDGYRI 227 d1j93a_ 203 F-DSWAtelspvdfeEFSLPYLKQIVDSVKlthpNLPLILYAsGSGG-lLERLpltGVDV 260 : :::: ::::::::::::::: :::::::: :::: :::: :::: d1iv8a2 228 DhIDGL---------YDPEKYINDLRSIIK----NXIIIVEK-ILGFqeELKL---NSDG 270 d1j93a_ 261 VSLD--WTVD-------------------------------------------------- 268 :::: :::: d1iv8a2 271 TTGYdfLNYSnllfnfnqeimdsiyenftaekisisesixkikaqiidelfsyevxrlas 330 d1j93a_ 269 ------------------------------------------------------------ 269 d1iv8a2 331 qlgisydilrdylscidvyrtyanqivkecdktneieeatkrnpeaytklqqympavyax 390 d1j93a_ 269 --------------------------------maDGRRRlGPNVAIQGNVD-----pGVL 291 ::::: ::::::::::: ::: d1iv8a2 391 ayedtflfrynrlisinevgsdlryykispdqfhVFNQK-RRGKITLNATSthdtkfSED 449 d1j93a_ 292 FG---------------------------------------------------------- 293 :: d1iv8a2 450 VRmkisvlsefpeewknxveewhsiinpkvsrndeyryyqvlvgsfyegfsndfxerixq 509 d1j93a_ 294 -----------------------------------------------------SKEFITN 300 ::::::: d1iv8a2 510 hmixsvreaxintswrnqnkeyenrvmelveetftnkdfiksfmkfesxirriGMIKSLS 569 d1j93a_ 301 RINDTVKKAgkgkHILNLgHGIK-VGTP-------------------------------- 327 ::::::::: ::::: :::: :::: d1iv8a2 570 LVALKIMSA----GIPDF-YQGTeIWRYlltdpdnrvpvdfkklheileksxkfeknmle 624 d1j93a_ 328 -----EENFAHFFEIAKGL--------ry 343 :::::::::::::: d1iv8a2 625 smddgRIKMYLTYXLLSLRkqlaedflkg 653 FAST alignment (Normalized score: 3.46 Raw score:1640.00) d1j93a_ 1 TQPLLLDAVRGKEVERP--PVWLMRQAGRYMKSYQLLCEKYPLFRDRSE--------NVD 50 :::: ::: d1iv8a2 1 -----------------MISATY--------------------------RLQLNKNFNFG 17 d1j93a_ 51 LVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 :::::::::::: ::::::: d1iv8a2 18 DVIDNLWYFADL-GVSHLYL---------------------------------------- 36 d1j93a_ 111 FIPEKS----------------------------VPYVGEALTILRKEVNN-QAAVLGFV 141 ::::::::::::: :::::::: d1iv8a2 37 ------SPVLMASPGSNHGYDVIDHSRINDELGGEKEYRRLIETAHT----IGLGIIQDI 86 d1j93a_ 142 GAPFTLASYVVEGGS--------------------------------------------- 156 d1iv8a2 87 ---------------VPNHMAVNSLNWRLMDVLAMGAASAYYTYFDFFPEDDKIRLPILG 131 d1j93a_ 157 ------------------------------------------------------------ 157 d1iv8a2 132 EDLDTVISKGLLKIVKDGDEYFLEYFKWKLPLTEVGNDIYDTLQKQNYTLMSWKNPPSYR 191 d1j93a_ 157 -SKNFTKIKRLAFAEPKV-------LHALLQKFATSMAKYIRYQADSGAQAVQIFDSWAT 208 :::::: :::::::::::::: :::::::: d1iv8a2 192 RFFDVNT-----------LIGVNVEADHVFQESHSAILD-------LDVDGYRI------ 227 d1j93a_ 209 ELSPVDFEEFSLP-------YLKQIVDSVKLTHPNLPLILYASGSGGLLERL-------P 254 :::::::::::::::::::::: : d1iv8a2 228 -------------DHIDGLYDPEKYINDLRSIIKNAIIIVEK----------ILGFQEEL 264 d1j93a_ 255 LTGVDVVSLDWTV----------------------------------------------- 267 ::::::::: d1iv8a2 265 KLNSDGTTG----YDFLNYSNLLFNFNQEIMDSIYENFTAEKISISESIAKIKAQIIDEL 320 d1j93a_ 268 ------------------------------------------------------------ 268 d1iv8a2 321 FSYEVARLASQLGISYDILRDYLSCIDVYRTYANQIVKECDKTNEIEEATKRNPEAYTKL 380 d1j93a_ 268 -----------------------------------------DMADGRRRLGPNVAIQGNV 286 :::::::: ::::::::: d1iv8a2 381 QQYMPAVYAAAYEDTFLFRYNRLISINEVGSDLRYYKISPDQFHVFNQK-RRGKITLNA- 438 d1j93a_ 287 DPGVLFG----------------------------------------------------- 293 d1iv8a2 439 -------TSTHDTKFSEDVRMKISVLSEFPEEWKNAVEEWHSIINPKVSRNDEYRYYQVL 491 d1j93a_ 294 ------------------------------------------------------------ 294 d1iv8a2 492 VGSFYEGFSNDFAERIAQHMIASVREAAINTSWRNQNKEYENRVMELVEETFTNKDFIKS 551 d1j93a_ 294 -----------SKEFITNRINDTVKKAGKGK--HILNLGHGIKVGT-------------- 326 :::::::::::::: :::: d1iv8a2 552 FMKFESAIRRIGMIKSLSLVALKIM------SAGIPD---------FYQGTEIWRYLLTD 596 d1j93a_ 327 -----------------------------------PEENFAHFFEIAKGLRY-------- 343 ::::::::::::: d1iv8a2 597 PDNRVPVDFKKLHEILEKSAKFEKNMLESMDDGRIKMYLTYALLSLRK----QLAEDFLK 652 d1j93a_ 344 - 344 d1iv8a2 653 G 653 TMalign alignment (TM-score: 0.54 Raw score:184.34) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 : : ::::: ::: ::::: ::::::: :::: d1iv8a2 1 ----M--I---------SATYR-LQL---------------NKNFN--FGDVIDN-LWYF 26 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKS-VPY 119 :::::::::: ::: ::: :::: ::::: : :: :::::: ::: d1iv8a2 27 ADLGVSHLYL-SPV-LMA------SPGS--NHGYD--V---------ID-HSRINDELGG 64 d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASY--V-------------------------- 151 :::::::::::::::::::::::::: :::: : d1iv8a2 65 EKEYRRLIETAHTIGLGIIQDIVPNH-MAVNSLNWRLMDVLAMGAASAYYTYFDFFPEDD 123 d1j93a_ 152 ---VEG------------------------------------------------------ 154 ::: d1iv8a2 124 KIRLPILGEDLDTVISKGLLKIVKDGDEYFLEYFKWKLPLTEVGNDIYDTLQKQNYTLMS 183 d1j93a_ 155 GSSKNFTKIKRLAFAEPKV---L-HALLQK----FATSMAKYIRYQADSGAQAVQIFDSW 206 ::::: ::::: : :::::: :::::::::::: ::::::::: d1iv8a2 184 -------WKNPP--SYRRFFDVNTLIGVNVEADHVFQESHSAILDL---DVDGYRIDH-- 229 d1j93a_ 207 ATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLD-W 265 : : ::::::::::::::::::::::::: :::::::::: :::::::: : d1iv8a2 230 I-------D---GLYDPEKYINDLRSIIKNAIIIVEK--ILGFQEELKL-NSDGTTGYDF 276 d1j93a_ 266 TVDM-------------------------------------------------------- 269 :::: d1iv8a2 277 LNYSNLLFNFNQEIMDSIYENFTAEKISISESIAKIKAQIIDELFSYEVARLASQLGISY 336 d1j93a_ 270 ------------------------------------------------------------ 270 d1iv8a2 337 DILRDYLSCIDVYRTYANQIVKECDKTNEIEEATKRNPEAYTKLQQYMPAVYAAAYEDTF 396 d1j93a_ 270 --------------------------ADGRRRLGPNVAIQGNVD------PGV--LF--- 292 :::::::::::::::::: ::: :: d1iv8a2 397 LFRYNRLISINEVGSDLRYYKISPDQFHVFNQKRRGKITLNATSTHDTKFSEDVRMKISV 456 d1j93a_ 293 ------------------------------------------------------------ 293 d1iv8a2 457 LSEFPEEWKNAVEEWHSIINPKVSRNDEYRYYQVLVGSFYEGFSNDFAERIAQHMIASVR 516 d1j93a_ 293 --------------------------------------------G-SKEFITNRINDTVK 307 : :::::::::::::: d1iv8a2 517 EAAINTSWRNQNKEYENRVMELVEETFTNKDFIKSFMKFESAIRRIGMIKSLSLVALKIM 576 d1j93a_ 308 KAGKGKHILNLGHGIK-VGT------------------------------------PEE- 329 :: ::::: :::: ::: ::: d1iv8a2 577 -SA---GIPDF-YQGTEIWRYLLTDPDNRVPVDFKKLHEILEKSAKFEKNMLESMDDGRI 631 d1j93a_ 330 NFAHFFEIAKGL--R---Y--- 343 :::::::::::: : : d1iv8a2 632 KMYLTYALLSLRKQLAEDFLKG 653 HHsearch alignment (Probability: 0.02 E-value:0.06) d1j93a_ 169 AEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDF 215 ::::::::::::: :::::::::: :::::::::::: d1iv8a2 205 EXDHVFQESHSXI-----------LDLDVDGYRI-DHIDGLYDPEKY 239