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 | d1kqpa_ | NH3-dependent NAD+-synthetase | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1h3fa1 | Tyrosyl-tRNA synthetase (TyrRS) | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 0.943 --> IntermediateDALI alignment (Z-score: 22.5 Raw score:2205.80) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1kqpa_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1kqpa_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1kqpa_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1kqpa_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1kqpa_ 1 -----------------------------------------------smqekimrelhvk 13 query 301 rldADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG-------aqN 353 ::::::::::::::::::::::::::::::::::::::::::::::: : d1kqpa_ 14 psiDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVEsireeggdaQ 73 query 354 VYGVSMPSKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAYMASL------GLTGLAE 406 ::::::::: :::: ::::::::::::: :::::::::::::::::: ::::::: d1kqpa_ 74 FIAVRLPHG-TQQD-EDDAQLALKFIKPdKSWKFDIKSTVSAFSDQYqqetgdQLTDFNK 131 query 407 ENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTlYGDSVGAYGPIKDVYKTSIFR 466 :::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1kqpa_ 132 GNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTkYGDGGADLLPLTGLTKRQGRT 191 query 467 LAEWRNraaaergqtppIPEASITK--------------------PDYPVLDAILELyvd 506 :::::: :::::::: :::::::::::: d1kqpa_ 192 LLKELG-----------APERLYLKeptadlldekpqqsdetelgISYDEIDDYLEG--- 237 query 507 rdtgadaivaaGYDRELVVKTLRMVDTAEYKRRQyppgtkisakgfgkdrrlPITNrwre 566 ::::::::::::::::::::::: :::: d1kqpa_ 238 ----------kEVSAKVSEALEKRYSMTEHKRQV------------pasmfdDWWK---- 271 query 567 gh 568 d1kqpa_ 272 -- 272 FAST alignment (Normalized score: 11.56 Raw score:4537.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1kqpa_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1kqpa_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1kqpa_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1kqpa_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1kqpa_ 1 ------------------------------------------------------------ 1 query 301 RLD----------------ADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAI 344 ::::::::::::::::::::::::::::::::::::::::: d1kqpa_ 1 ---SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRL 57 query 345 ACDALGAQ-----------NVYGVSMPSKYSSDH-SKGDAAELARRTG-LNFRTVSIEPM 391 :::: :::::::::::: ::::::::::::: ::::::::::: d1kqpa_ 58 AQLA----VESIREEGGDAQFIAVRLPHGTQ---QDEDDAQLALKFIKPDKSWKFDIKST 110 query 392 FDAYMAS------LGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTL 445 ::::::: ::::::::::::::::::::::::::::::::::::::::::: d1kqpa_ 111 VSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTG---- 166 query 446 Y-----GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTP-PIPEASITK-------- 491 :::::::::::::::::::::::: :::::::: d1kqpa_ 167 -FFTKYGDGGADLLPLTGLTKRQGRTLLKE------------LGAPERLYL-KEPTADLL 212 query 492 -------------PDYPVLDAILELYVDRDTGADAIVA--AGYDRELVVKTLRMVDTAEY 536 :::::::::: :::::::::::::::::::: d1kqpa_ 213 DEKPQQSDETELGISYDEIDDYL---------------EGKEVSAKVSEALEKRYSMTEH 257 query 537 KRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------ 568 :: d1kqpa_ 258 KR------------------------------QVPASMFDDWWK 271 TMalign alignment (TM-score: 0.37 Raw score:209.57) query 1 -------SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVE 53 d1kqpa_ 1 SMQEKIM----------------------------------------------------- 7 query 54 DLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAA 113 d1kqpa_ 8 ------------------------------------------------------------ 8 query 114 VLHRGRVALTFAKHHLPNYGV--FDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGR 171 : d1kqpa_ 8 --------------------REL------------------------------------- 10 query 172 VPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGD 231 ::::: d1kqpa_ 11 -------------------HVKPS------------------------------------ 15 query 232 SIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYE 291 d1kqpa_ 16 ------------------------------------------------------------ 16 query 292 AELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGA 351 ::::::::::::::::::::::::::::::::::::::::::::::::: d1kqpa_ 16 -----------IDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVES 64 query 352 -------QNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAYMASL---- 399 :::::::::::::: : ::::::::::::: :::::::::::::::::: d1kqpa_ 65 IREEGGDAQFIAVRLPHGTQQ-D-EDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQET 122 query 400 --GLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIK 457 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1kqpa_ 123 GDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLT 182 query 458 DVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK--------------------PDYPVL 497 ::::::::::::::: :::::::: :::::: d1kqpa_ 183 GLTKRQGRTLLKELG-----------APERLYLKEPTADLLDEKPQQSDETELGISYDEI 231 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY----PPGTKISAKGFG 553 :::::: : : ::::::::::::::::::::::: d1kqpa_ 232 DDYLEG----------K--E-VSAKVSEALEKRYSMTEHKRQVPASMF------------ 266 query 554 KDRRLPITNRWREGH 568 ::::: d1kqpa_ 267 ---DDWWK------- 271 HHsearch alignment (Probability: 1.00 E-value:0.00) query 297 GYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDAL------- 349 :::::::::::: :::::::::::::::::::::::::::::::::::::::: d1kqpa_ 11 HVKPSIDPKQEI-EDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEG 69 query 350 GAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFR-TVSIEPMFDAYMASLGL------T 402 ::::::::::: :::::::::::::::::::::: ::::::::::::::::: : d1kqpa_ 70 GDAQFIAVRLP--HGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLT 127 query 403 GLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKT 462 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1kqpa_ 128 DFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKR 187 query 463 SIFRLAEWRNRAAAERGQTPPIPEASI---TK-------PDYPVLDAILELYVDRDTGAD 512 ::::::::: ::::::::::::::::: :: :::::::::::: d1kqpa_ 188 QGRTLLKEL-GAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEG--------- 237 query 513 AIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGT 545 :::::::::::::::::::::: :::::: d1kqpa_ 238 ----KEVSAKVSEALEKRYSMTEHKR-QVPASM 265
Intermediate <-- 0.726 --> HitDALI alignment (Z-score: 4.6 Raw score:576.60) d1kqpa_ 1 smqekimrelhvkpsidpkqeIEDR-vnflkqYVKKTG----aKGFVLGISG-----gqd 50 :::: :::::: ::::::::: d1h3fa1 1 ----------ghtpeealallKRGAeeivpeeELLAKLkegrpLTVKLGADPtrpdlhlg 50 d1kqpa_ 51 stLAGRLAQLAVESIreeggdAQFIAVRLPHgtqqDEDDAQLALKFIK--------pDKS 102 ::::::::::::: :::::::::: ::::::::::::: ::: d1h3fa1 51 haVVLRKMRQFQELG------HKVVLIIGDF----TRENAKTYVAQAGkilrqephlFEL 100 d1kqpa_ 103 WKFD--IKSTvsAFSDQY------------------qqetgdqlTDFNkGNVKARTRMIA 142 :::: :::: :::::: :::: ::::::::::: d1h3fa1 101 RYNSewLEGL--TFKEVVrltslmtvaqmleredfkkryeagipISLH-ELLYPFAQAYD 157 d1kqpa_ 143 QYAIGgqegLLVLGTDHaaeavtgfftkYGDGG-------------aDLLPlTGLTK--- 186 ::::: :::::::: ::::: :::: ::::: d1h3fa1 158 SVAIR---aDVEMGGTD---------qrFNLLVgrevqraygqspqvCFLM-PLLVGldg 204 d1kqpa_ 187 -RQGR--------------------------------tllkelgaperlylkeptadlld 213 :::: d1h3fa1 205 rEKMSksldnyiglteppeamfkklmrvpdpllpsyfrlltdleeeeieallkagpvpah 264 d1kqpa_ 214 ekpqqsdetelgisydeiddylegkevsakvsealekrysmtehkrqvpasmfddwwk 271 d1h3fa1 265 rvlarlltaayalpqippridrafyeslgyaweafgrdkeagpeevrraearydevak 322 FAST alignment (Normalized score: 2.35 Raw score:695.10) d1kqpa_ 1 SMQEKIMRELHVKPSIDPKQEIEDRVNFL--------------------KQYVK---KTG 37 ::::: ::: d1h3fa1 1 -----------------------------GHTPEEALALLKRGAEEIVPEEELLAKLKEG 31 d1kqpa_ 38 AK-GFVLGIS-----GGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQ-DEDDA 90 :: ::::::: ::::::::::::::::: ::::::::::: ::::: d1h3fa1 32 RPLTVKLGADPTRPDLHLGHAVVLRKMRQFQE------LGHKVVLIIGD-----FTRENA 80 d1kqpa_ 91 QLALKFIKP-----------DKSWKFDIKSTVSAFS------------------------ 115 :::::: ::::: d1h3fa1 81 KTYVAQ---AGKILRQEPHLFELRY-----------NSEWLEGLTFKEVVRLTSLMTVAQ 126 d1kqpa_ 116 ------DQYQQETGDQLTDF-NKGNVKARTRMIAQYAIGGQEG-LLVLGTDHAAEAVTGF 167 :::::::::: :::: ::::::::::::::: ::::: d1h3fa1 127 MLEREDFKKRYEAGIP----ISLHE---LLYPFAQAYDSVAIRADVEMG----------- 168 d1kqpa_ 168 FTK-----YGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDET 222 ::::: d1h3fa1 169 ---GTDQRFNLLV----------------------------------------------- 178 d1kqpa_ 223 ELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK----------- 271 d1h3fa1 179 -------------------------------------------------GREVQRAYGQS 189 d1kqpa_ 272 ------------------------------------------------------------ 272 d1h3fa1 190 PQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEE 249 d1kqpa_ 272 ------------------------------------------------------------ 272 d1h3fa1 250 EEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEE 309 d1kqpa_ 272 ------------- 272 d1h3fa1 310 VRRAEARYDEVAK 322 TMalign alignment (TM-score: 0.41 Raw score:109.98) d1kqpa_ 1 --------SMQEKIMRELHVKPSIDPKQEIEDRV--N--F-LKQYVKKTGAKGFVLGIS- 46 ::::::: : : :::::::::::::::::: d1h3fa1 1 GHTPEEAL-------------------ALLKRGAEEIVPEEELLAKLKEGRPLTVKLGAD 41 d1kqpa_ 47 ---G-G-QDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDE-DDAQLALKFIKP- 99 : : :::::::::::::::: :::::::::::::::: :::::::::::: d1h3fa1 42 PTRPDLHLGHAVVLRKMRQFQEL-------GHKVVLIIGDFTRENAKTYVAQAGKILRQE 94 d1kqpa_ 100 --DKSWKFDIKSTVSAFSDQYQ-------------------------QETGDQLTDFNKG 132 :::::::::::::::::::: :::::: d1h3fa1 95 PHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGI-------PISLHE 147 d1kqpa_ 133 NVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGG-------ADLLPLTGLT 185 ::::::::::::::: :::::::: :: :::::::::: ::::::: :: d1h3fa1 148 LLYPFAQAYDSVAIR----ADVEMGGT--DQ--RFNLLVGREVQRAYGQSPQVCFLM-PL 198 d1kqpa_ 186 KR-------------------------------------QGRTLLKEL------------ 196 :: ::::::::: d1h3fa1 199 LVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKA 258 d1kqpa_ 197 ------------G--APE------------------------------------------ 200 : ::: d1h3fa1 259 GPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYD 318 d1kqpa_ 201 ----RLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTE 256 d1h3fa1 319 EVAK-------------------------------------------------------- 322 d1kqpa_ 257 HKRQVPASMFDDWWK 271 d1h3fa1 323 --------------- 323 HHsearch alignment (Probability: 0.02 E-value:1.70) d1kqpa_ 16 IDPKQEIEDR---------VNFLKQYVKKTGAKGFVLGI--SGG---QDSTLAGRLAQLA 61 :::::::::: :::::::::::::::::::: ::: ::::::::::::: d1h3fa1 2 HTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQF 61 d1kqpa_ 62 VESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSW 103 :: :::::::::::::::::::::::::::::::::: d1h3fa1 62 QE------LGHKVVLIIGDFTRENAKTYVAQAGKILRQEPHL 97