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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jila_ | Tyrosyl-tRNA synthetase (TyrRS) | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1ivsa4 | Valyl-tRNA synthetase (ValRS) | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 0.690 --> IntermediateDALI alignment (Z-score: 6.1 Raw score:653.80) query 1 ---dadeeVYSAL-----vvglrayvAKNGFRSVLIGLS-----ggIDSALVAAIACDAL 47 ::::: ::::::::::::: :::::::::::::: d1jila_ 1 tnvliedlKWRGLiyqqtdeqgiedlLNKEQVTLYCGADptadslhIGHLLPFLTLRRFQ 60 query 48 G-aqNVYGVSMP--SKYS----------------SDHSKGDAAELARRTG-------LNF 81 : :::::::: :::: :::::::::::::::: ::: d1jila_ 61 EhghRPIVLIGGgtGMIGdpsgkseervlqteeqVDKNIEGISKQMHNIFefgtdhgAVL 120 query 82 RTVS--IEPMfdAYMASL----------------------gltGLAEENLQSRLRGTTLM 117 :::: :::: :::::: ::::::::::::::::: d1jila_ 121 VNNRdwLGQI--SLISFLrdygkhvgvnymlgkdsiqsrlehgISYTEFTYTILQAIDFG 178 query 118 AISNQEGH-IVLAPGNkselavgystlyGDSV--------------gAYGPiKDVY---- 158 :::::::: ::::::: :::: :::: :::: d1jila_ 179 HLNRELNCkIQVGGSD---------qwgNITSgielmrrmygqtdayGLTI-PLVTksdg 228 query 159 ----------------------------------ktsifrLAEW---------------- 168 :::: d1jila_ 229 kkfgksesgavwldaektspyefyqfwinqsdedvikflkYFTFlgkeeidrleqsknea 288 query 169 --------rnRAAAerGQTPpipeasitkpdypvldailelyvdrdtgadaivaagydre 220 :::: :::: d1jila_ 289 phlreaqktlAEEV--TKFI---------------------------------------- 306 query 221 lvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jila_ 307 -----------------------------hgedalndairisqalf 323 FAST alignment (Normalized score: 2.35 Raw score:689.80) query 1 DADEEVYSA------------------LVVGLRAYVAKNGF--RSVLIGLSG-------- 32 ::::::::::: :::::: d1jila_ 1 ---------TNVLIEDLKWRGLIYQQTDEQGIEDLLNK---EQVTLYCG---ADPTADSL 45 query 33 ---GIDSALVAAIACDALGAQ-NVYGVSMPSKYS-------------------------- 62 ::::::::::::: :::::::: d1jila_ 46 HIGHLLPFLTLRRFQE-----HGHRPIVLI----GGGTGMIGDPSGKSEERVLQTEEQVD 96 query 63 --SDHSKGDAAELARRTGL-------NFRTVSIEPMFDAYMASLGLTG------------ 101 ::::::::::: ::::::::::::: d1jila_ 97 KNIEGISKQMHNI------FEFGTDHGAVLVNNRDWLGQ---------ISLISFLRDYGK 141 query 102 ---------------------LAEENLQSRLRGTTLMAISNQEGHIVLA---PGNKSELA 137 :::::::::::::::::::::::: :::: d1jila_ 142 HVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELNC----KIQVGGS---- 193 query 138 VGYSTLY-GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLD 196 :::: d1jila_ 194 -------DQWGN------------------------------------------------ 198 query 197 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRL 256 d1jila_ 199 ------------------------------------------------------------ 199 query 257 PITNRWREGH-------------------------------------------------- 266 d1jila_ 199 ----------ITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSP 248 query 267 ------------------------------------------------------------ 267 d1jila_ 249 YEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHG 308 query 267 --------------- 267 d1jila_ 309 EDALNDAIRISQALF 323 TMalign alignment (TM-score: 0.46 Raw score:121.20) query 1 ------DADEEVYSALV--VG--L--RAYVAKNGFRSVLIGLSG----G-IDSALVAAIA 43 :::::::: : : :::::::::::::::::: : :::::::::: d1jila_ 1 TNVLIE---DLKWRGLIYQ-QTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTL 56 query 44 CDALG-AQNVYGVSMPS--K------------YS----S-DHSKGDAAELARRTG----- 78 ::::: ::::::::::: : :: : ::::::::::::::: d1jila_ 57 RRFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDH 116 query 79 -LNFRTVS--IEPMFDAYMASL-----------------------GLTGLAEENLQSRLR 112 ::::::: :::: ::::::: ::::::::::::: d1jila_ 117 GAVLVNNRDWLGQI-SLISFLRDYGKHVGVNYMLGKDSIQSRLEH--GISYTEFTYTILQ 173 query 113 GTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS-VG------------AYGPIKDVYK 159 :::::::::::::::::::: :: : : ::: :: ::::: ::: d1jila_ 174 AIDFGHLNRELNCKIQVGGS--DQ--W--G--NITSGIELMRRMYGQTDAYGLTI--PLV 223 query 160 TS-----IF-----------------------------R---LAEWRN------------ 170 :: :: : :::::: d1jila_ 224 TKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQ 283 query 171 -------------RAAAERGQTPP----------------IPEASITKPDYPVLDAILEL 201 ::::::::::: d1jila_ 284 SKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF-------------------- 323 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1jila_ 324 ------------------------------------------------------------ 324 query 262 WREGH 266 d1jila_ 324 ----- 324 HHsearch alignment (Probability: 0.02 E-value:0.47) query 163 FRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVA--AGYDRE 220 :::::::::::::::::::::::::::: ::::::::::::::::::::::: :::::: d1jila_ 203 IELMRRMYGQTDAYGLTIPLVTKSDGKK-FGKSESGAVWLDAEKTSPYEFYQFWINQSDE 261 query 221 LVVKTLRMV 229 ::::::::: d1jila_ 262 DVIKFLKYF 270
Intermediate <-- 1.735 --> HitDALI alignment (Z-score: 9.4 Raw score:1221.60) d1jila_ 1 ----tnvliedlkwrgliyqqtdeqgiedllnKEQVTLYCG-ADPTAdSLHIGHLLPFLT 55 ::::::::: ::::: :::::::::::: d1ivsa4 1 mdlpkaydpksvepkwaekwaknpfvanpksgKPPFVIFMPpPNVTG-SLHMGHALDNSL 59 d1jila_ 56 LRRFQEHG------HRPIVLIGggTGMIGdpsgkseeRVLQ------------------- 90 :::::::: :::::::: ::::: :::: d1ivsa4 60 QDALIRYKrmrgfeAVWLPGTD--HAGIA-------tQVVVerlllkegktrhdlgrekf 110 d1jila_ 91 ---TEEQVDKNIEGISKQMHN-IFEFGTdhgaVLVNNRD-WLGQIslisFLRD------- 138 :::::::::::::::::: :::::: ::::::: ::::: :::: d1ivsa4 111 lerVWQWKEESGGTILKQLKRlGASADW---sREAFTMDeKRSRAvryaFSRYyheglay 167 d1jila_ 139 -----ygkhvgvnymLGKDsIQSRL----------------------------------- 158 :::: ::::: d1ivsa4 168 raprlvnwcprcettLSDL-EVETCsrcgtpieyaifpqwwlrmrplaeevlkglrrgdi 226 d1jila_ 159 --------------------ehgISYT--------------------------------- 165 :::: d1ivsa4 227 afvperwkkvnmdwlenvkdwniSRQLwwghqipawycedcqavnvprperyledptsce 286 d1jila_ 166 ------------EFTYTILQAIDFGHLN--------RELN--CKIQVGGSDQWG-NITSG 202 :::::::::::::::: :::: :::::::::::: ::::: d1ivsa4 287 acgsprlkrdedVFDTWFSSALWPLSTLgwpeetedLKAFypGDVLVTGYDILFlWVSRM 346 d1jila_ 203 IELMRRMYGQTDA-YGLTIPLVTKSdGKKFG-ksesGAVWLDAektsPYEFyqfwinqsd 260 ::::::::::::: ::::::::::: ::::: ::::::: :::: d1ivsa4 347 EVSGYHFMGERPFkTVLLHGLVLDE-KGQKMskskgNVIDPLE--mvERYG--------- 394 d1jila_ 261 edvikfLKYFTflgkeeidrleqskneaphlreaqKTLAEEvtkfihgedalndairisq 320 ::::: :::::: d1ivsa4 395 -adalrFALIY---------latggqdirldlrwlEMARNF------------------- 425 d1jila_ 321 alf 323 d1ivsa4 426 --- 426 FAST alignment (Normalized score: 5.22 Raw score:1936.00) d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLN-------------------------------- 28 d1ivsa4 1 ----------------------------MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSG 32 d1jila_ 29 KEQVTL-YCGADPTADSLHIGHLLPFLTLRRFQE------HGHRPIVLIGGGTGMIGDPS 81 :::::: :::::: :::::::::::::::::::: :::::::::: d1ivsa4 33 KPPFVIFMPPPNV-TGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTD---------- 81 d1jila_ 82 GKSEERVLQ--------------------------------TEEQVDKNIEGISKQMHNI 109 :::::::::::::::::: d1ivsa4 82 ---------HAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKR- 131 d1jila_ 110 FEFGTDHG-------AVLVNN-RDWLGQISLISFL---RDYGKHVGVNYMLGKDSIQSR- 157 :::::: ::::: :::::: d1ivsa4 132 --------LGASADWSREAFTMDEKRS--------RAVRYAFSR---------------Y 160 d1jila_ 158 ---------------------------LEHGISYTEF----------------------- 167 :::: d1ivsa4 161 YHEGLAYRAPRLVNWCPRCETTLSDLEVETC------SRCGTPIEYAIFPQWWLRMRPLA 214 d1jila_ 168 ------------------------------------------------------------ 168 d1ivsa4 215 EEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPR 274 d1jila_ 168 --------------------------TYTILQAIDFGHLNRE-------------LNCKI 188 ::::::::::::: ::::: d1ivsa4 275 PERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLST---LGWPEETEDLKAFYPGDV 331 d1jila_ 189 QVGGSDQW-GNITSGIELMRRMYGQTD----AYGLTIPLVTKSDGKKFGKSES-----GA 238 :::::::: ::::::::::::::: ::::::::::::::::: :: d1ivsa4 332 LVTGYDILFLWVSRMEVSGYHFMG---ERPFKTVLLHGLVLDEKGQKM-----SKSKGNV 383 d1jila_ 239 VWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTL 298 ::: d1ivsa4 384 IDP--------------------------------------------------------- 386 d1jila_ 299 AEEVTKFIHGEDALNDAIRISQALF----------------------------------- 323 d1ivsa4 387 -------------------------LEMVERYGADALRFALIYLATGGQDIRLDLRWLEM 421 d1jila_ 324 ---- 324 d1ivsa4 422 ARNF 425 TMalign alignment (TM-score: 0.53 Raw score:171.96) d1jila_ 1 ---------------------------------TNVLIEDLKWRGLIYQQTDEQGIEDLL 27 d1ivsa4 1 MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGK--------------------------- 33 d1jila_ 28 NKEQVTLYC-GADPTADSLHIGHLLPFLTLRRFQ-EHG-----HRPIVLIGGGTGMIGDP 80 ::::::: :::::: ::::::::::::::::: ::: :::::::: :: :::: d1ivsa4 34 --PPFVIFMPPPNVTG-SLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTD--HA-GIAT 87 d1jila_ 81 SGKSEERVLQ---------------------TEEQVDKNIEGISKQMHN-IFEFGTDHGA 118 ::::: :::::::::::::::::: :::::: : d1ivsa4 88 -----QVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADW---S 139 d1jila_ 119 VLVNNRD-WLGQISLISFLRDYG-KHVGV---N--YML---------GKDSIQS-RL--- 158 ::::::: ::::::: ::::::: ::::: : : :::::: :: d1ivsa4 140 REAFTMDEKRSRAVR-YAFSRYYHEGLAYRAPRLV--NWCPRCETTL-SDLEVETCSRCG 195 d1jila_ 159 -EHGI-----------------------------------------------S-YT-E-- 166 :::: : :: : d1ivsa4 196 TPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWW 255 d1jila_ 167 --------------------------------------------FTYTILQAIDFGHLN- 181 ::::::::::::::: d1ivsa4 256 GHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLG 315 d1jila_ 182 R-----EL--NC-K-IQVGGSDQWG-NITSGIELMRRMYGQTDAY-GLTIPLVTKSDGKK 230 : :: :: : :::::::::: ::::::::::::::::::: :::::::::::::: d1ivsa4 316 WPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQK 375 d1jila_ 231 FGK--SESGAVWLDAEKTSPYEFY--QFWI-NQSDEDVIKFLKYFT--------FLGKEE 277 ::: :::::::: :::: :: :: :::::::: d1ivsa4 376 MSKSK--GNVIDPLE--MVER-YGAD--ALR-------FALIYLATGGQDIRLD------ 415 d1jila_ 278 IDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF 323 :::::::::: d1ivsa4 416 --------------LRWLEMARNF---------------------- 425 HHsearch alignment (Probability: 0.98 E-value:0.00) d1jila_ 28 NKEQVTLYCGA-DPTADSLHIGHLLPFL----TLRRFQEHGHRPIVLIGGGTG 75 ::::::::::: ::::: :::::::::: ::::::::::::::::::::: d1ivsa4 32 GKPPFVIFMPPPNVTGS-LHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHA 83