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 | d1n3la_ | Tyrosyl-tRNA synthetase (TyrRS) | 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 <-- 1.922 --> HitDALI alignment (Z-score: 21.2 Raw score:2311.00) d1jila_ 1 ---TNVLIEDLKwrGLIYQQTDEQGIEDLLNKEQVTLYCGADPTAdSLHIGHLLPFLTLR 57 ::::::::: ::::::::::::::::::::::::::::::: :::::::::::::: d1n3la_ 1 apsPEEKLHLIT--RNLQEVLGEEKLKEILKERELKIYWGTATTG-KPHVAYFVPMSKIA 57 d1jila_ 58 RFQEHGHRPIVLIGGGTGMIGdpsgkseerVLQTEEQVDKNIEGISKQMHNIFE--fgTD 115 ::::::::::::::::::::: :::::::::::::::::::::::: :: d1n3la_ 58 DFLKAGCEVTILFADLHAYLD--------nMKAPWELLELRVSYYENVIKAMLEsigvPL 109 d1jila_ 116 HGAVLVNNRDWLGQIS-LISFLrDYGKHVGVNYMLG--KDSIQSRleHGISYTEFTYTIL 172 :::::::::::::::: ::::: ::::::::::::: ::::::: ::::::::::::: d1n3la_ 110 EKLKFIKGTDYQLSKEyTLDVY-RLSSVVTQHDSKKagAEVVKQV--EHPLLSGLLYPGL 166 d1jila_ 173 QAIDFGHLNrelnCKIQVGGSDQWGNITSGIELMRRMYgQTDAYGLTIPLVTksdgkkFG 232 ::::::::: ::::::::::::::::::::::::: ::::::::::::: :: d1n3la_ 167 QALDEEYLK----VDAQFGGIDQRKIFTFAEKYLPALG-YSKRVHLMNPMVP------GL 215 d1jila_ 233 KSeSGAVWLDaekTSPYEFYQFWINQSD-------EDVIKFLKYFT--FLGK-------- 275 :: ::::::: ::::::::::::::: ::::::::::: :::: d1n3la_ 216 TGsESKIDLL---DRKEDVKKKLKKAFCepgnvenNGVLSFIKHVLfpLKSEfvilrdek 272 d1jila_ 276 -------EEIDRLEQSKNEAPHLR-EAQKTLAEEVTKFIHG----edalndairisqalf 323 ::::::::::::::::: :::::::::::::::: d1n3la_ 273 wggnktyTAYVDLEKDFAAEVVHPgDLKNSVEVALNKLLDPirekfntpalkklasaayp 332 FAST alignment (Normalized score: 14.22 Raw score:4658.00) d1jila_ 1 ---TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLR 57 :::::::::: :::::::::::::::::::::::::::::: :::::::::::::: d1n3la_ 1 APSPEEKLHLITR--NLQEVLGEEKLKEILKERELKIYWGTATTG-KPHVAYFVPMSKIA 57 d1jila_ 58 RFQEHGHRPIVLIGGGTGMIGDPSGKSEERV----LQTEEQVDKNIEGISKQMHNIFEFG 113 ::::::::::::::::::: ::::::::::::::::::::: d1n3la_ 58 DFLKAGCEVTILFADLHAY------------LDNMKAPWELLELRVSYYENVIKAM---- 101 d1jila_ 114 TDH---------GAVLVNNRDWLGQI---SLISFLRDYGKHVGVNYMLGKDSIQSRLE-- 159 :::::::::::: :::::: ::::::::::::: d1n3la_ 102 ---LESIGVPLEKLKFIKGTDYQL--SKEYTLDVY-RLSSVVTQHDSKK---------AG 146 d1jila_ 160 -------HGISYTEFTYTILQAIDFGHLNRELNCKIQVGGSDQWGNITSGIELMRRMYGQ 212 :::::::::::::::::::: ::::::::::::::::::::::::: ::: d1n3la_ 147 AEVVKQVEHPLLSGLLYPGLQALDEEY----LKVDAQFGGIDQRKIFTFAEKYLPA-LGY 201 d1jila_ 213 T-DAYGLTIPLVTKSDGKKFGKSES-------GAVWLDAEKTSPYEFYQFWINQSD---- 260 :::::::::: ::::: :::::::::::::: d1n3la_ 202 -SKRVHLMNPMV-------------PGLTGSESKIDL---LDRKEDVKKKLKKA--FCEP 242 d1jila_ 261 -----EDVIKFLKYFTFLGKE-----------------------EIDRLEQSKNEAPHL- 291 :::::::::: :::::::::: d1n3la_ 243 GNVENNGVLSFIKHV------LFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFA-----A 291 d1jila_ 292 -----REAQKTLAEEVTKFIHGEDALNDAIRISQALF---------------------- 323 :::::::::::::: d1n3la_ 292 EVVHPGDLKNSVEVALNKL------------------LDPIREKFNTPALKKLASAAYP 332 TMalign alignment (TM-score: 0.72 Raw score:231.59) d1jila_ 1 ---TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLR 57 ::::::::: : :::::::::::::::::::::::::::::: :::::::::::::: d1n3la_ 1 APSPEEKLHLIT-R-NLQEVLGEEKLKEILKERELKIYWGTATTG-KPHVAYFVPMSKIA 57 d1jila_ 58 RFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFE--F-GT 114 ::::::::::::::::::::: ::::::::::::::::::::::::: : : d1n3la_ 58 DFLKAGCEVTILFADLHAYLD--------NMKAPWELLELRVSYYENVIKAMLESIGV-P 108 d1jila_ 115 DHGAVLVNNRDWLGQISLISFLRDYGKHVGVNYMLGK-DSIQSRLEHGISYTEFTYTILQ 173 ::::::::::::::::::::::::::::::::::::: ::::::: :::::::::::::: d1n3la_ 109 LEKLKFIKGTDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQV-EHPLLSGLLYPGLQ 167 d1jila_ 174 AIDFGHLNRELNCKIQVGGSDQWGNITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGK 233 :::::::: :::::::::::::::::::::::::::: :::::::::: ::: d1n3la_ 168 ALDEEYLK----VDAQFGGIDQRKIFTFAEKYLPALGYSK-RVHLMNPMVP------GLT 216 d1jila_ 234 SESGAVWLDAEKTSPYEFYQFWI-NQS-D--E--D-VIKFLKYFT--FLGK--------- 275 :::::::: : ::::::::::: ::: : : : ::::::::: :::: d1n3la_ 217 GSESKIDL-L--DRKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKW 273 d1jila_ 276 ----EEIDR-LE-QSK-NEAPHLREAQKTLAEEVTKFIHGEDA----------------L 312 ::::: :: ::: :::::::::::::::::::::::::: d1n3la_ 274 GGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYP- 332 d1jila_ 313 NDAIRISQALF 323 d1n3la_ 333 ----------- 333 HHsearch alignment (Probability: 1.00 E-value:0.00) d1jila_ 6 EDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLRRFQEHGHR 65 :::::::: ::::::::::::::::::::::::::::: ::::::::::::::::::::: d1n3la_ 8 LHLITRNL-QEVLGEEKLKEILKERELKIYWGTATTGK-PHVAYFVPMSKIADFLKAGCE 65 d1jila_ 66 PIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDHGAVLVNNRD 125 :::::::::::::::::::::: :::::::::::::::::::: :::::::::::: d1n3la_ 66 VTILFADLHAYLDNMKAPWELL----ELRVSYYENVIKAMLESIGV--PLEKLKFIKGTD 119 d1jila_ 126 WLGQISLISFLRDYGKHVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELN 185 :::::::::::::::::::::::::::::::::::::::::::::::::::::: :: d1n3la_ 120 YQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEY----LK 175 d1jila_ 186 CKIQVGGSDQWGNITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEK 245 ::::::::::::::::::::::::::::::::::::::::::::::::::: d1n3la_ 176 VDAQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGSESKIDLLD--------- 226 d1jila_ 246 TSPYEFYQFWI-------NQSDEDVIKFLK-----------------YFTFLGKEEIDRL 281 :::::::::: :::::::::::: ::::::::::::: d1n3la_ 227 -RKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDL 285 d1jila_ 282 EQSKNEA-PHLREAQKTLAEEVTKFIHGEDA 311 ::::::: ::::::::::::::::::::::: d1n3la_ 286 EKDFAAEVVHPGDLKNSVEVALNKLLDPIRE 316