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 | d1vl2a1 | Argininosuccinate synthetase, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1jila_ | Tyrosyl-tRNA synthetase (TyrRS) | Nucleotidylyl transferase | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 1.669 --> IntermediateDALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 0.996 --> HitDALI alignment (Z-score: 7.9 Raw score:769.60) d1vl2a1 1 ------------------------------KEKVVLAYS-----GGLDTSVILKWLCEKG 25 ::::::::: :::::::::::::::: d1jila_ 1 tnvliedlkwrgliyqqtdeqgiedllnkeQVTLYCGADptadsLHIGHLLPFLTLRRFQ 60 d1vl2a1 26 ---FDVIAYVA-NVGQ-------------------KDDFVAIKEKALKTG------aSKV 56 :::::::: :::: ::::::::::::::: ::: d1jila_ 61 ehgHRPIVLIGgGTGMigdpsgkseervlqteeqvDKNIEGISKQMHNIFefgtdhgAVL 120 d1vl2a1 57 YVED--LRREfVTDY------------iftallgnaMYEGRYLLGTAIARPLIAKRQVEI 102 :::: :::: :::: :::::::::::::::::::::::: d1jila_ 121 VNNRdwLGQIsLISFlrdygkhvgvnymlgkdsiqsRLEHGISYTEFTYTILQAIDFGHL 180 d1vl2a1 103 AEKEGAQYVAHGATgkgnDQVRFELTYAALN-----PNLKVISPWK-------------- 143 :::::::::::::: ::::::::::::: :::::::::: d1jila_ 181 NRELNCKIQVGGSD----QWGNITSGIELMRrmygqTDAYGLTIPLvtksdgkkfgkses 236 d1vl2a1 144 -----------------------dpeflAKFK---------------------------t 153 :::: d1jila_ 237 gavwldaektspyefyqfwinqsdedviKFLKyftflgkeeidrleqskneaphlreaqk 296 d1vl2a1 154 dliNYAMEKG--------------ipi 166 ::::::: d1jila_ 297 tlaEEVTKFIhgedalndairisqalf 323 FAST alignment (Normalized score: 5.45 Raw score:1261.00) d1vl2a1 1 ------------------------------KEKVVLAYSG---------GLDTSVILKWL 21 ::::::::: ::::::::::: d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGAD-PTADSLHIGHLLPFLTLRRF 59 d1vl2a1 22 CEKGFDVIAYVANVGQKD--------------------------DFVAIKEKALKTGA-- 53 :::::::::::: ::::::::::: d1jila_ 60 QEHGHRPIVLIG------GGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHN---IF 110 d1vl2a1 54 -------SKVYVED--------LRREFVTDYIFTALLGNA----------------MYEG 82 ::::: :::::::::: :::: d1jila_ 111 EFGTDHGAVLVN--NRDWLGQISLISFLRDYG--------KHVGVNYMLGKDSIQSRLEH 160 d1vl2a1 83 RYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----GNDQVRFELTYAAL--NPNL 136 ::::::::::::::::::::::::::::::: :::::::::::::: :::: d1jila_ 161 GISYTEFTYTILQAIDFGHLNRELNCKIQVG-----GSDQWGNITSGIELMRRMYGQTDA 215 d1vl2a1 137 KVISPWKDPEFLAKFKTD------------------------------------------ 154 :::: d1jila_ 216 YGLT--------------IPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDE 261 d1vl2a1 155 ------------------------------------LINYAMEKGIPI------------ 166 ::::::: d1jila_ 262 DVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTK-----FIHGEDALNDAI 316 d1vl2a1 167 ------- 167 d1jila_ 317 RISQALF 323 TMalign alignment (TM-score: 0.67 Raw score:110.56) d1vl2a1 1 ------------------------------KEKVVLAYS----GGL-DTSVILKWLCEK- 24 ::::::::: ::: :::::::::::: d1jila_ 1 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLRRFQ 60 d1vl2a1 25 G--FDVIAYVAN-V-G-------------Q---KD--DFVAIKEKALKTGA------SKV 56 : ::::::::: : : : :: :::::::::::::: ::: d1jila_ 61 EHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDHGAVL 120 d1vl2a1 57 YVED--LRREFVT--DY---IFT----------------ALLGNAMYEGRYLLGTAIARP 93 :::: :::: :: :: : ::::::::::::::: d1jila_ 121 VNNRDWLGQI-SLISFLRDY--GKHVGVNYMLGKDSIQS------RLEHGISYTEFTYTI 171 d1vl2a1 94 LIAKRQVEIAEKEGAQYVAHGATGKGNDQVRFELTYAAL-----NPNLKVISPWKDPEFL 148 ::::::::::::::::::::::: :::::::::::: :::::::::: : d1jila_ 172 LQAIDFGHLNRELNCKIQVGGSD----QWGNITSGIELMRRMYGQTDAYGLTIP-----L 222 d1vl2a1 149 AKFKT-----DL------I---------------N--------------YA--------- 159 ::: :: : : :: d1jila_ 223 --VTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDR 280 d1vl2a1 160 ------------------M-EK--GIP----------------I 166 : :: ::: d1jila_ 281 LEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF- 323 HHsearch alignment (Probability: 0.01 E-value:0.31) d1vl2a1 15 SVILKWLCEKGFDVIAYVANVGQ 37 ::::::::::::::::::::::: d1jila_ 53 FLTLRRFQEHGHRPIVLIGGGTG 75